I did some testing to get some debugging info for you, so here it goes. This is the full dmesg output I get when I plug my DFP in up to the point where it disappears from /dev/input.
Wheel plugged in
ehci_hcd 0000:00:1d.7: BAR 0: set to [mem 0xf2504c00-0xf2504fff] (PCI address [0xf2504c00-0xf2504fff])
ehci_hcd 0000:00:1d.7: restoring config space at offset 0xf (was 0x100, writing 0x10a)
ehci_hcd 0000:00:1d.7: restoring config space at offset 0x1 (was 0x2900000, writing 0x2900002)
ehci_hcd 0000:00:1d.7: PME# disabled
ehci_hcd 0000:00:1d.7: PCI INT A -> GSI 23 (level, low) -> IRQ 23
ehci_hcd 0000:00:1d.7: setting latency timer to 64
ehci_hcd 0000:00:1a.7: BAR 0: set to [mem 0xf2504800-0xf2504bff] (PCI address [0xf2504800-0xf2504bff])
ehci_hcd 0000:00:1a.7: restoring config space at offset 0xf (was 0x300, writing 0x30a)
ehci_hcd 0000:00:1a.7: restoring config space at offset 0x1 (was 0x2900000, writing 0x2900002)
ehci_hcd 0000:00:1a.7: PME# disabled
ehci_hcd 0000:00:1a.7: PCI INT C -> GSI 19 (level, low) -> IRQ 19
ehci_hcd 0000:00:1a.7: setting latency timer to 64
ehci_hcd 0000:00:1a.7: PCI INT C disabled
ehci_hcd 0000:00:1a.7: PME# enabled
uhci_hcd 0000:00:1d.0: PCI INT A -> GSI 23 (level, low) -> IRQ 23
uhci_hcd 0000:00:1d.0: setting latency timer to 64
usb 6-1: new low speed USB device using uhci_hcd and address 2
usbcore: registered new interface driver usbhid
usbhid: USB HID core driver
input: Logitech Logitech Driving Force as /devices/pci0000:00/0000:00:1d.0/usb6/6-1/6-1:1.0/input/input9
logitech 0003:046D:C294.0001: input,hidraw0: USB HID v1.00 Joystick [Logitech Logitech Driving Force] on usb-0000:00:1d.0-1/input0
hid_logitech: Force feedback for Logitech force feedback devices by Johann Deneux <johann.deneux@it.uu.se>
ehci_hcd 0000:00:1d.7: PCI INT A disabled
ehci_hcd 0000:00:1d.7: PME# enabled
Set to native command sent
usb 6-1: USB disconnect, address 2
logitech 0003:046D:C294.0002: parse failed
ehci_hcd 0000:00:1d.7: BAR 0: set to [mem 0xf2504c00-0xf2504fff] (PCI address [0xf2504c00-0xf2504fff])
ehci_hcd 0000:00:1d.7: restoring config space at offset 0xf (was 0x100, writing 0x10a)
ehci_hcd 0000:00:1d.7: restoring config space at offset 0x1 (was 0x2900000, writing 0x2900002)
ehci_hcd 0000:00:1d.7: PME# disabled
ehci_hcd 0000:00:1d.7: PCI INT A -> GSI 23 (level, low) -> IRQ 23
ehci_hcd 0000:00:1d.7: setting latency timer to 64
ehci_hcd 0000:00:1a.7: BAR 0: set to [mem 0xf2504800-0xf2504bff] (PCI address [0xf2504800-0xf2504bff])
ehci_hcd 0000:00:1a.7: restoring config space at offset 0xf (was 0x300, writing 0x30a)
ehci_hcd 0000:00:1a.7: restoring config space at offset 0x1 (was 0x2900000, writing 0x2900002)
ehci_hcd 0000:00:1a.7: PME# disabled
ehci_hcd 0000:00:1a.7: PCI INT C -> GSI 19 (level, low) -> IRQ 19
ehci_hcd 0000:00:1a.7: setting latency timer to 64
ehci_hcd 0000:00:1a.7: PCI INT C disabled
ehci_hcd 0000:00:1a.7: PME# enabled
usb 6-1: new low speed USB device using uhci_hcd and address 3
ehci_hcd 0000:00:1d.7: PCI INT A disabled
ehci_hcd 0000:00:1d.7: PME# enabled
logitech 0003:046D:C298.0003: timeout initializing reports
input: Logitech Logitech Driving Force Pro as /devices/pci0000:00/0000:00:1d.0/usb6/6-1/6-1:1.0/input/input10
logitech 0003:046D:C298.0003: input,hidraw0: USB HID v1.00 Joystick [Logitech Logitech Driving Force Pro] on usb-0000:00:1d.0-1/input0
hid_logitech: Force feedback for Logitech force feedback devices by Johann Deneux <johann.deneux@it.uu.se>
ehci_hcd 0000:00:1d.7: PCI INT A disabled
ehci_hcd 0000:00:1d.7: PME# enabled
Another command sent (disabling autocenter in this case, but it doesn't matter which)
logitech 0003:046D:C298.0004: parse failed
logitech: probe of 0003:046D:C298.0004 failed with error -110
Now the device is gone from /dev/input and even rmmoding the USB drivers doesn't make it reappear. I attached a simple communication log I got with USBLyzer, the log should contain all important commands. The OS I captured it on was Win7 x64. There is a lot of junk (sorry) because I tried to move the wheel to see how it reports position of its axes. If you read it carfefully, I'll see why the separate pedals cannot work without some modification of the drivers or a userspace hack. (you'll have to change the extension to .html to read it)
I did another test which makes me think there is a bug in linux USB HID layer. I installed Logitech drivers for my DFP to a virtualboxed Win7 x86 and tried to initialize the wheel from there. Windows drivers successfully send the commands, the wheel switches to the native mode and then I virtualbox gives an error message similar to the one in dmesg. This makes me believe that LTWC does everything right, but DFP behaves somewhat weird during reconnecting and confuses the linux USB HID layer....