Here is the usb relaed dmesg, it's a bit long ,
Maybe i need to look into the schematics, see why the VBUS power is lost 
after driver initailzed, the power is on before booting up linux.

Thanks
lei

ehci_hcd: block sizes: qh 128 qtd 96 itd 192 sitd 96
PCI: enabling device 0000:00:0d.2 (0140 -> 0142)
PCI: Enabling bus mastering for device 0000:00:0d.2
ehci_hcd 0000:00:0d.2: EHCI Host Controller
drivers/usb/core/inode.c: creating file 'devices'
drivers/usb/core/inode.c: creating file '001'
ehci_hcd 0000:00:0d.2: new USB bus registered, assigned bus number 1
ehci_hcd 0000:00:0d.2: reset hcs_params 0x2192 dbg=0 cc=2 pcc=1 ports=2
ehci_hcd 0000:00:0d.2: reset portroute 1 0
ehci_hcd 0000:00:0d.2: reset hcc_params 0012 thresh 1 uframes 256/512/1024
PCI: Enabling Mem-Wr-Inval for device 0000:00:0d.2
ehci_hcd 0000:00:0d.2: MWI active
ehci_hcd 0000:00:0d.2: ...powerdown ports...
ehci_hcd 0000:00:0d.2: supports USB remote wakeup
ehci_hcd 0000:00:0d.2: irq 28, io mem 0x4b002000
ehci_hcd 0000:00:0d.2: reset command 080002 (park)=0 ithresh=8 period=1024 
Reset
 HALT
ehci_hcd 0000:00:0d.2: init command 010009 (park)=0 ithresh=1 period=256 RUN
ehci_hcd 0000:00:0d.2: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004
usb usb1: default language 0x0409
usb usb1: new device strings: Mfr=3, Product=2, SerialNumber=1
usb usb1: Product: EHCI Host Controller
usb usb1: Manufacturer: Linux 2.6.17.8 ehci_hcd
usb usb1: SerialNumber: 0000:00:0d.2
usb usb1: uevent
usb usb1: configuration #1 chosen from 1 choice
usb usb1: adding 1-0:1.0 (config #1, interface 0)
usb 1-0:1.0: uevent
hub 1-0:1.0: usb_probe_interface
hub 1-0:1.0: usb_probe_interface - got id
hub 1-0:1.0: USB hub found
hub 1-0:1.0: 2 ports detected
hub 1-0:1.0: standalone hub
hub 1-0:1.0: individual port power switching
hub 1-0:1.0: individual port over-current protection
hub 1-0:1.0: Single TT
hub 1-0:1.0: TT requires at most 8 FS bit times (666 ns)
hub 1-0:1.0: power on to power good time: 20ms
hub 1-0:1.0: local power source is good
hub 1-0:1.0: enabling power on all ports
<5>ehci_irq: status=0x00000004
PCD deteted, i=2
command=10009
status=0
status=1803
hub 1-0:1.0: state 7 ports 2 chg 0000 evt 0000
drivers/usb/core/inode.c: creating file '001'
ohci_hcd: 2005 April 22 USB 1.1 'Open' Host Controller (OHCI) Driver (PCI)
ohci_hcd: block sizes: ed 64 td 64
ehci_hcd 0000:00:0d.2: GetStatus port 1 status 001002 POWER sig=se0 CSC
hub 1-0:1.0: port 1, status 0100, change 0001, 12 Mb/s
PCI: enabling device 0000:00:0d.0 (0140 -> 0142)
PCI: Enabling bus mastering for device 0000:00:0d.0
ohci_hcd 0000:00:0d.0: OHCI Host Controller
drivers/usb/core/inode.c: creating file '002'
ohci_hcd 0000:00:0d.0: new USB bus registered, assigned bus number 2
ohci_hcd 0000:00:0d.0: addr=0x4b000004
ohci_hcd 0000:00:0d.0: 0x0
ohci_hcd 0000:00:0d.0: created debug files
ohci_hcd 0000:00:0d.0: irq 28, io mem 0x4b000000
ohci_hcd 0000:00:0d.0: resetting from state 'reset', control = 0x0
ohci_hcd 0000:00:0d.0: OHCI controller state
ohci_hcd 0000:00:0d.0: OHCI 1.0, NO legacy support registers
ohci_hcd 0000:00:0d.0: control 0x083 HCFS=operational CBSR=3
ohci_hcd 0000:00:0d.0: cmdstatus 0x00000 SOC=0
ohci_hcd 0000:00:0d.0: intrstatus 0x00000044 RHSC SF
ohci_hcd 0000:00:0d.0: intrenable 0x8000001a MIE UE RD WDH
ohci_hcd 0000:00:0d.0: hcca frame #01fe
ohci_hcd 0000:00:0d.0: roothub.a ff000201 POTPGT=255 NPS NDP=1(1)
ohci_hcd 0000:00:0d.0: roothub.b 00000000 PPCM=0000 DR=0000
ohci_hcd 0000:00:0d.0: roothub.status 00008000 DRWE
ohci_hcd 0000:00:0d.0: roothub.portstatus [0] 0x00000100 PPS
usb usb2: default language 0x0409
usb usb2: new device strings: Mfr=3, Product=2, SerialNumber=1
usb usb2: Product: OHCI Host Controller
usb usb2: Manufacturer: Linux 2.6.17.8 ohci_hcd
usb usb2: SerialNumber: 0000:00:0d.0
usb usb2: uevent
usb usb2: configuration #1 chosen from 1 choice
usb usb2: adding 2-0:1.0 (config #1, interface 0)
usb 2-0:1.0: uevent
hub 2-0:1.0: usb_probe_interface
hub 2-0:1.0: usb_probe_interface - got id
hub 2-0:1.0: USB hub found
hub 2-0:1.0: 1 port detected
hub 2-0:1.0: standalone hub
hub 2-0:1.0: no power switching (usb 1.0)
hub 2-0:1.0: global over-current protection
hub 2-0:1.0: power on to power good time: 510ms
hub 2-0:1.0: local power source is good
hub 2-0:1.0: no over-current condition exists
hub 1-0:1.0: debounce: port 1: total 100ms stable 100ms status 0x100
hub 2-0:1.0: state 7 ports 1 chg 0000 evt 0000
drivers/usb/core/inode.c: creating file '001'
PCI: enabling device 0000:00:0d.1 (0140 -> 0142)
PCI: Enabling bus mastering for device 0000:00:0d.1
ohci_hcd 0000:00:0d.1: OHCI Host Controller
drivers/usb/core/inode.c: creating file '003'
ohci_hcd 0000:00:0d.1: new USB bus registered, assigned bus number 3
ohci_hcd 0000:00:0d.1: addr=0x4b001004
ohci_hcd 0000:00:0d.1: 0x0
ohci_hcd 0000:00:0d.1: created debug files
ohci_hcd 0000:00:0d.1: irq 28, io mem 0x4b001000
ohci_hcd 0000:00:0d.1: resetting from state 'reset', control = 0x0
ohci_hcd 0000:00:0d.1: OHCI controller state
ohci_hcd 0000:00:0d.1: OHCI 1.0, NO legacy support registers
ohci_hcd 0000:00:0d.1: control 0x083 HCFS=operational CBSR=3
ohci_hcd 0000:00:0d.1: cmdstatus 0x00000 SOC=0
ohci_hcd 0000:00:0d.1: intrstatus 0x00000044 RHSC SF
ohci_hcd 0000:00:0d.1: intrenable 0x8000001a MIE UE RD WDH
ohci_hcd 0000:00:0d.1: hcca frame #01fe
ohci_hcd 0000:00:0d.1: roothub.a ff000201 POTPGT=255 NPS NDP=1(1)
ohci_hcd 0000:00:0d.1: roothub.b 00000000 PPCM=0000 DR=0000
ohci_hcd 0000:00:0d.1: roothub.status 00008000 DRWE
ohci_hcd 0000:00:0d.1: roothub.portstatus [0] 0x00000100 PPS
usb usb3: default language 0x0409
usb usb3: new device strings: Mfr=3, Product=2, SerialNumber=1
usb usb3: Product: OHCI Host Controller
usb usb3: Manufacturer: Linux 2.6.17.8 ohci_hcd
usb usb3: SerialNumber: 0000:00:0d.1
usb usb3: uevent
usb usb3: configuration #1 chosen from 1 choice
usb usb3: adding 3-0:1.0 (config #1, interface 0)
usb 3-0:1.0: uevent
hub 3-0:1.0: usb_probe_interface
hub 3-0:1.0: usb_probe_interface - got id
hub 3-0:1.0: USB hub found
hub 3-0:1.0: 1 port detected
hub 3-0:1.0: standalone hub
hub 3-0:1.0: no power switching (usb 1.0)
hub 3-0:1.0: global over-current protection
hub 3-0:1.0: power on to power good time: 510ms
hub 3-0:1.0: local power source is good
hub 3-0:1.0: no over-current condition exists
hub 3-0:1.0: state 7 ports 1 chg 0000 evt 0000
drivers/usb/core/inode.c: creating file '001'
Initializing USB Mass Storage driver...
usbcore: registered new driver usb-storage
USB Mass Storage support registered.

----- Original Message ----- 
From: "Alan Stern" <[EMAIL PROTECTED]>
To: "Lei Sun" <[EMAIL PROTECTED]>
Cc: <Linux-usb-users@lists.sourceforge.net>
Sent: Wednesday, March 14, 2007 4:49 PM
Subject: Re: [Linux-usb-users] problem with EHCI controller


> On Wed, 14 Mar 2007, Lei Sun wrote:
>
>> > On Wed, 14 Mar 2007, Lei Sun wrote:
>> >
>> >> Thanks for your reply! Appreciate it !
>> >>
>> >> the debugging code in ehci_hub_status_data() shows that the port 
>> >> status
>> >> always return "0x1000" with or without flah devices plugged in.
>> >
>> > That disagrees with what you said earlier:
>> >
>> >>>> 3. Read port status register (2 ports total), port#1 return 0, 
>> >>>> port#2
>> >>>> returned 1002,  by looking at the code bellow:
>> >
>> > You said the port status was 0x1002, not 0x1000.
>>
>> status was 0x1002, that was print it out in ehci_irq() funtion last time,
>> ( i didn't put debugging message in ehci_hub_status_data() by that time).
>> now ehci_irq() function print out "0x1803" instead,
>> and 0x1000 is print out in ehci_hub_status_data() function.  I even 
>> disagree
>> with what I saw, because it doesn't seems to be consistent.
>>
>> We did had some hardware issue, the chip was stressed by higher voltage.
>> But since i am still able to read/write PCI register, i am assuming it 
>> still
>> function correctly.
>
> Can you post another dmesg log with CONFIG_USB_DEBUG turned on, showing
> what happens when you plug the device in?
>
>> > When the device is plugged in, the port status should have the 0x0001 
>> > bit
>> > set (PORT_CONNECT).  You may have to wait a few milliseconds for it to
>> > debounce.  And when you first plug in the device, the 0x0002 bit should
>> > also be set (PORT_CSC).
>>
>> What about the PORT_RESUME bit?  is it suppose to be set when device 
>> plugged
>> in ?
>
> It is not supposed to be set.
>
>> >> i was mistaken by saying "port was powering down" , it is he USB power 
>> >> i
>> >> was
>> >> talking about, we have a LED indicating the USB power , it was turned 
>> >> off
>> >> right after usb was initialized. Is that suppose to be like this?
>> >
>> > What do you mean by "USB power"?  Do you mean power to the EHCI
>> > controller?  Do you mean VBUS power on the USB port?  Do you mean
>> > something else?
>>
>> VBUS power
>
> Either VBUS power should always be on (if the controller doesn't do power
> switching) or it should be on whenever PORT_POWER (0x1000) is enabled.
> Since that bit was enabled, VBUS power should have been on.
>
> Alan Stern
> 


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