This problem still exists in Linux 3.13.0-32-generic #56-Ubuntu SMP Mon
Jul 7 11:32:12 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

For the record, the symptom that drew me here was the failure to create
a /dev/dvb device. I do not know if the IR device was working.

It does appear to be motherboard related. I have two HVR4000s working in
another machine. A third one worked in yet another machine. On two
identical, but newer motherboards the third one fails intermittently.

For the record, the actual structure of the suggested option file is:
$ cat /etc/modprobe.d/cx88xx.conf 
options cx88xx i2c_debug=1
options cx88xx i2c_scan=1

The debug option may be omitted.

Logs can be posted if required, but I suspect a bug with this longevity,
affecting obsolete hardware and with only two subscribers is probably
best abandoned.

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https://bugs.launchpad.net/bugs/836062

Title:
  [media/video] cx88xx HVR-1300,HVR-3000, HVR-4000 tveeprom: Huh, no
  eeprom present

Status in “linux” package in Ubuntu:
  Fix Released

Bug description:
  A long-standing bug still affecting kernel v3.1-rc3 (affects Ubuntu
  from Hardy through Oneiric) that occurs during boot where the
  Hauppauge cx88xx device fails to read the EEPROM using
  tveeprom_read(), which results in the Infra-Red receiver failing to be
  initialised, amongst other problems.

  WORKAROUND:
  
https://bugs.launchpad.net/ubuntu/+source/linux/+bug/836062/+attachment/2331923/+files/cx88xx.conf

  add the cx88xx module option:
  i2c_scan=1

  and copy the attached file to:
  /etc/modprobe.d/cx88xx.conf

  A related fix for LP bug #439163 "HVR-1300 HVR-3000 HVR-4000 broken in
  kernel" submitted to the main-line kernel by Devin Heitmueller of
  Kernel Labs (commit: 2d196931 in v3.0) addresses a related issue
  (opening/closing of the tuner frontends in rapid succession causes
  channel scan failures) but doesn't solve this issue.

  The cause appears to be failure to correctly initialise the tuner's
  i2c bus, or gracefully handle errors from i2c_transfer().

  I'm currently working with mainline kernels from Linus' tree with
  Mythbuntu 11.04 Natty to trace the issue and hopefully resolve it for
  an HVR-4000. If I can resolve it in main-line hopefully the patch can
  be backported to LTS releases.

  [    0.000000] Linux version 3.1.0-0301rc3-generic (root@zinc) (gcc version 
4.2.3 (Ubuntu 4.2.3-2ubuntu7)) #201108231005 SMP Tue Au
  g 23 11:10:27 UTC 2011
  ...
  [    9.901908] IR NEC protocol handler initialized
  [    9.938166] cx88/2: cx2388x MPEG-TS Driver Manager version 0.0.9 loaded
  [    9.938266] cx88[0]: quirk: PCIPCI_TRITON -- set TBFX
  [    9.938271] cx88[0]: quirk: PCIPCI_ALIMAGIK -- latency fixup
  [    9.938286] cx88[0]: setting pci latency timer to -1
  [    9.943547] cx88/0: cx2388x v4l2 driver version 0.0.9 loaded
  [    9.964453] cx88[0]: subsystem: 0070:6902, board: Hauppauge WinTV-HVR4000 
DVB-S/S2/T/Hybrid [card=68,autodetected], frontend(s): 2
  [    9.964463] cx88[0]: TV tuner type 63, Radio tuner type -1
  [    9.964468] cx88[0]: cx88_reset
  [   10.015789] IR RC5(x) protocol handler initialized
  [   10.041429] IR RC6 protocol handler initialized
  [   10.082720] IR JVC protocol handler initialized
  [   10.112795] IR Sony protocol handler initialized
  [   10.148789] IR MCE Keyboard/mouse protocol handler initialized
  [   10.176078] lirc_dev: IR Remote Control driver registered, major 250
  [   10.182052] IR LIRC bridge handler initialized
  [   10.436710] cx88[0]: i2c register ok
  [   10.436720] cx88[0]: i2c init: enabling analog demod on HVR1300/3000/4000 
tuner
  [   10.692251] i2c-core: driver [tuner] using legacy suspend method
  [   10.692259] i2c-core: driver [tuner] using legacy resume method
  [   11.060383] EXT4-fs (sda3): re-mounted. Opts: errors=remount-ro
  [   11.079076] cx2388x alsa driver version 0.0.9 loaded
  [   11.270057] tveeprom 1-0050: Huh, no eeprom present (err=-6)?
  [   11.270071] tveeprom 1-0050: Encountered bad packet header [00]. Corrupt 
or not a Hauppauge eeprom.
  [   11.270077] cx88[0]: warning: unknown hauppauge model #0
  [   11.270081] cx88[0]: hauppauge eeprom: model=0
  ...
  [   11.652049] Registered IR keymap rc-hauppauge
  [   11.652871] input: cx88 IR (Hauppauge WinTV-HVR400 as 
/devices/pci0000:00/0000:00:0d.2/rc/rc0/input5
  [   11.653178] rc0: cx88 IR (Hauppauge WinTV-HVR400 as 
/devices/pci0000:00/0000:00:0d.2/rc/rc0
  [   12.348467] input: MCE IR Keyboard/Mouse (cx88xx) as 
/devices/virtual/input/input6
  [   12.350773] rc rc0: lirc_dev: driver ir-lirc-codec (cx88xx) registered at 
minor = 0
  [   12.350785] cx88[0]/2: cx2388x 8802 Driver Manager
  [   12.350802] cx88-mpeg driver manager 0000:00:0d.2: enabling device (0014 
-> 0016)
  [   12.351385] ACPI: PCI Interrupt Link [LNKF] enabled at IRQ 11
  [   12.351395] cx88-mpeg driver manager 0000:00:0d.2: PCI INT A -> Link[LNKF] 
-> GSI 11 (level, low) -> IRQ 11
  [   12.351408] cx88[0]/2: found at 0000:00:0d.2, rev: 5, irq: 11, latency: 
255, mmio: 0xc8000000
  [   12.351504] cx8800 0000:00:0d.0: enabling device (0014 -> 0016)
  [   12.351514] cx8800 0000:00:0d.0: PCI INT A -> Link[LNKF] -> GSI 11 (level, 
low) -> IRQ 11
  [   12.351525] cx88[0]/0: found at 0000:00:0d.0, rev: 5, irq: 11, latency: 
32, mmio: 0xca000000
  ...
  [   12.773653] wm8775 1-001b: chip found @ 0x36 (cx88[0])
  [   12.847981] cx88[0]: set_tvnorm: "NTSC-M" fsc8=28636360 adc=28636363 
vdec=28636360 db/dr=28636360/28636360
  [   12.847994] cx88[0]: set_pll:    MO_PLL_REG       0x00fffffe 
[old=0x00f15f18,freq=28636360]
  [   12.848013] cx88[0]: pll locked [pre=2,ofreq=28636360]
  [   12.848019] cx88[0]: set_tvnorm: MO_INPUT_FORMAT  0x00000001 
[old=0x00000000]
  [   12.848026] cx88[0]: set_tvnorm: MO_OUTPUT_FORMAT 0x181f0008 
[old=0x181f0000]
  [   12.848033] cx88[0]: set_tvnorm: MO_SCONV_REG     0x00020000 
[old=0x00021f07]
  [   12.848039] cx88[0]: set_tvnorm: MO_SUB_STEP      0x00400000 
[old=0x0043e0f8]
  [   12.848045] cx88[0]: set_tvnorm: MO_SUB_STEP_DR   0x00400000 
[old=0x00538e38]
  [   12.848052] cx88[0]: set_tvnorm: MO_AGC_BURST     0x00007270 
[old=0x00006d63,bdelay=114,agcdelay=112]
  [   12.848059] cx88[0]: set_tvnorm: MO_HTOTAL        0x0000038e 
[old=0x0000135a,htotal=910]
  [   12.848067] cx88[0]: set_scale: 320x240 [TB,NTSC-M]
  [   12.848071] cx88[0]: set_scale: hdelay  0x0038 (width 754)
  [   12.848075] cx88[0]: set_scale: hscale  0x15b3
  [   12.848078] cx88[0]: set_scale: hactive 0x0140
  [   12.848082] cx88[0]: set_scale: vdelay  0x0018
  [   12.848085] cx88[0]: set_scale: vscale  0x1e00
  [   12.848089] cx88[0]: set_scale: vactive 0x01e0
  [   12.848095] cx88[0]: set_scale: filter  0x80009
  [   12.896662] cx88[0]/0: registered device video1 [v4l2]
  [   12.896900] cx88[0]/0: registered device vbi0
  [   12.896970] cx88_audio 0000:00:0d.1: enabling device (0014 -> 0016)
  [   12.896991] cx88_audio 0000:00:0d.1: PCI INT A -> Link[LNKF] -> GSI 11 
(level, low) -> IRQ 11
  [   12.897042] cx88[0]/1: CX88x/0: ALSA support for cx2388x boards
  [   12.897740] snd_cmipci 0000:00:05.0: enabling device (0084 -> 0085)
  [   12.897756] snd_cmipci 0000:00:05.0: PCI INT A -> Link[LNKF] -> GSI 11 
(level, low) -> IRQ 11
  [   12.937107] snd_cmipci 0000:00:0a.0: enabling device (0084 -> 0085)
  [   12.937668] ACPI: PCI Interrupt Link [LNKC] enabled at IRQ 10
  [   12.937675] PCI: setting IRQ 10 as level-triggered
  [   12.937684] snd_cmipci 0000:00:0a.0: PCI INT A -> Link[LNKC] -> GSI 10 
(level, low) -> IRQ 10
  ...
  [   13.712708] cx88/2: cx2388x dvb driver version 0.0.9 loaded
  [   13.712717] cx88/2: registering cx8802 driver, type: dvb access: shared
  [   13.712727] cx88[0]/2: subsystem: 0070:6902, board: Hauppauge 
WinTV-HVR4000 DVB-S/S2/T/Hybrid [card=68]
  [   13.712734] cx88[0]/2: cx2388x based DVB/ATSC card
  [   13.712740] cx8802_alloc_frontends() allocating 2 frontend(s)
  [   14.657161] tuner-simple 1-0061: creating new instance
  [   14.657173] tuner-simple 1-0061: type set to 63 (Philips FMD1216ME MK3 
Hybrid Tuner)
  [   14.661849] DVB: registering new adapter (cx88[0])
  [   14.661868] DVB: registering adapter 0 frontend 0 (Conexant 
CX24116/CX24118)...
  [   14.676705] DVB: registering adapter 0 frontend 1 (Conexant CX22702 
DVB-T)...

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