Hi David
 
I had your problem, I think it's because of the core i3 or up processors. I 
tried  to use cygwin on some computers that are core i3, core i5 and core i7 
and I had the same problem, but when I used the dual core computer it hadn't 
this problem. I'm working now with my dual core computer.
About your second question, the jflashmm is used by default, I don't know why 
but is used before the USBLoaderHost, so you should just install the jfalshmm 
by folowing this instructions:
 
1)go to "c:\cygwin\opt\tinyos-2.x-contrib\intelmote2\  
tools\platforms\intelmote2\jflashmm"  and extract the file "jflashmm.tgz"
 
2)copy the files "jflashmm.exe ;  Flash_8810_1_16.DAT ; bulbcx16.DAT" in the 
directory "C:\ cygwin\bin".
 
3) finaly double click on the file "restore restore-bootloader.BAT "
 
After that you'll have your first problem I had a procedure to solve it but I 
don't know if it's really good, Ididn't try it. I found this, you can find some 
answers here:
 
The following is copied from 
http://www.cse.wustl.edu/wsn/index.php?title=Installing_the_Imote2_USB_Boot_Loader

The Imote2 [1] platform comes with a USB boot loader that allows you to install 
an application over USB. This is significantly faster and more reliable than 
using JTAG. The boot loader is written in C and is OS-independent. For 
technical details on the boot loader, see module 
tinyos-1.x/contrib/imote2/tools/src/ within the TinyOS 1.x CVS repository. In 
particular, look at files "bootloader.doc" and "bootloader_install.txt". 
Checking Whether the USB Boot Loader is Installed 
You can check whether the USB boot loader is installed by using USBLoaderHost 
to try to program an image onto the mote. If the USB Boot Loader is installed, 
the process should be successful. If the the USB Boot loader is not installed, 
USBLoaderHost will get stuck printing "Device Detected" as shown below. $ 
USBLoaderHost -p build/imote2/main.bin.out
Program Mode, File name = build/imote2/main.bin.out
File Size 178204
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
Device detected
...

Follow the sections below to install the USB Boot Loader. 
Installing the USB Boot Loader 
The following instructions assume you are running Microsoft Windows XP, it does 
NOT work in Windows Vista. 
In order to install the boot loader, you must have an IIB2400 interface board 
[2] and a JTAG programmer. Connect the USB and JTAG cables to the interface 
board, then attach the interface board to the Imote2. Note that it is important 
to plug the USB cable into the interface board, NOT the Imote2. Connect the 
other end of the JTAG cable to your computer's parallel port. Ensure your 
parallel port is set to ECP mode at base 0x378 [3]. 
 
Imote2 ready to be reprogrammed using JTAG
Crossbow Technologies provides a convenient pre-packaged script that automates 
the installation of the USB boot loader. You can download it here: 

http://www.xbow.com/Support/wobjectDetail.aspx?id=50160000000KXVYAA4&type=Solution&page=0
 
Download and extract the zip archive "imote2-jflashmm.zip" to a known location 
on your computer. Then navigate to the extracted files and run the script 
called "restore-bootloader.bat". Be patient! The installation process can take 
over 45 minutes! 
Here is the output of a successful installation: C:\Documents and 
Settings\Liang Fok\Desktop\imote2-jflashmm>restore-bootloader.b
at

C:\Documents and Settings\Liang Fok\Desktop\imote2-jflashmm>JFlashmm.exe bulbcx1
6 attributes.bin P 0x1E00000

JFLASH Version 5.01.007
COPYRIGHT (C) 2000 - 2003 Intel Corporation

PLATFORM SELECTION:
 Processor= PXA27x
 Development System= Mainstone
 Data Version= 1.00.001

PXA27x revision C5
Found flash type: 28F256L18B

Erasing block at address 1e00000
Erasing block at address 1e20000
Erasing block at address 1e40000
Erasing block at address 1e60000
Erasing block at address 1e80000
Erasing block at address 1ea0000
Erasing block at address 1ec0000
Erasing block at address 1ee0000
Starting programming
Using BUFFER programming mode...
Writing flash at hex address 1edfb00, 99.86% done
Programming done
Starting Verify
Verifying flash at hex address 1edfe04, 99.94% done
Verification successful!

C:\Documents and Settings\Liang Fok\Desktop\imote2-jflashmm>JFlashmm.exe bulbcx1
6 vector.bin P

JFLASH Version 5.01.007
COPYRIGHT (C) 2000 - 2003 Intel Corporation

PLATFORM SELECTION:
 Processor= PXA27x
 Development System= Mainstone
 Data Version= 1.00.001

PXA27x revision C5
Found flash type: 28F256L18B

Erasing block at address 0
Starting programming
Using BUFFER programming mode...

Programming done
Starting Verify

Verification successful!

C:\Documents and Settings\Liang Fok\Desktop\imote2-jflashmm>JFlashmm.exe bulbcx1
6 txtdata.bin P 0x200000

JFLASH Version 5.01.007
COPYRIGHT (C) 2000 - 2003 Intel Corporation

PLATFORM SELECTION:
 Processor= PXA27x
 Development System= Mainstone
 Data Version= 1.00.001

PXA27x revision C5
Found flash type: 28F256L18B

Erasing block at address 200000
Starting programming
Using BUFFER programming mode...
Writing flash at hex address 21dc80, 98.81% done
Programming done
Starting Verify
Verifying flash at hex address 21de96, 99.24% done
Verification successful!

Potential Pitfall 1: Giveio Error
The installation script fails with the following error: JFLASH Version 5.01.007
COPYRIGHT (C) 2000 - 2003 Intel Corporation

PLATFORM SELECTION:
 Processor= PXA27x
 Development System= Mainstone
 Data Version= 1.00.001

Couldn't access giveio device

This occurs when giveio.sys is not installed on your computer. Windows XP and 
other similar operating systems do not provide direct access to your computer's 
parallel port. giveio.sys is a service that provides direct access to the 
parallel port, and is needed by JFlashmm. To install giveio.sys, first install 
WinAVR, then run "install_giveio.bat" within C:\WinAVR\bin\. 

On Windows Vista, be sure to run install_giveio.bat as an Administrator. 
 
                                          
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