[Kindle Fire Q&A, Help & Troubleshooting] lolunix:
I too get this, I've been through what feels like every thread on here about this, only a few of these show up as the 'usb boot only' though and they all end in no answer. I have tried all forms of partitioning up to and including dd'n the p1.img over top of xloader and p2.img on top of bootloader.

With usb, i can go back fully stock (however, even fully stock wont boot without usb boot.. so its got to be busted xloader or bootloader), i can get TWRP installed, any ROM and its all usable.. until as OP said.. power out or reboot needed. It's bothering me enough just wanting to fix it I keep rebreaking perfectly good installs thinking some nugget I found/missed re-reading endless posts is the one.. just in case someone else comes through with this, here are my findings:

happened to me as originally I bricked to the point had to crack it open and short it to get it to boot via usb, finally working well using liveUSB firekit. However, from that point on, would NEVER boot on its own, and would NEVER shutdown/reboot without needing 20-30s of power button molestation. perhaps this is left over issue of the pin short... dunno

Once i figured out I could usbboot, basically went on with everything as normal. recovery, roms, back to stock, back to rom, etc etc. What seemingly never works, or simply oui can never get to, is the bootloader. All indications that I have known/been able to check seem to think its iinstalling, perhaps we are just never making it to it (xloader death)

So then I went crazy and tried everything from adb/fastboot raw on Mac, windows and linux, setting bootmode to 4000 every way with every tool listed on this site possible.. no joy.. usbboot is a must. Tried zeroing the mmcblk0p1/p2 and writing good versions on top, nothing.

Current state.. if I, via adb/fastboot/twrp/recovery do a reboot or shutdown.. the kindle shuts down screen and led's only (sometimes even leaving the green power light on, but almost ALWAYS just all black, but not off) .. dmesg notes that its stuck in a usb connect/disconnect loop, with an error:

new high-speed USB device number 33 using ehci_hcd

unable to get BOS descriptor

New USB device found, idVendor=0451, idProduct=d00f

New USB device strings: Mfr=33, Product=37, SerialNumber=0

Product: OMAP4430

Manufacturer: Texas Instruments

USB disconnect, device number 33

rinse, repeat, about every 3 seconds.

As you can see, BOS descriptor can't be found.. which is just a little stupid because the port its plugged into is 2.0

bcdUSB 2.00

but maybe there is still something there? not changing any port though, usbboot has no problem.

I sniffed the traffic of the usb bus while plugging in the USB cable after shutting down via 30 second hold, and its pretty much the same thing, just bouncing the connection before it has time to get started.. so it seems to be hitting this "issue" both on shutdown/reboot and startup. As I can't really tell, with usb being the only way for me to talk to the KF, I can only assume after a hard shutdown when I push the button again its probably doing the same thing (no lights, no screen), but I can confirm once I plug in the usb and it tries to boot itself.

Only sort of difference is sometimes it can go down into the dark reboot and I am able to run usbboot and it comes back up (usb never unplugged) but its been sporadic so I haven't chased it.

At this point I just want to figure out exactly what bit needs flipped in the front somewhere so I can reboot my KF like all the cool kids so I'll probably keep hacking on this issue until I really really brick it or hopefully help comes along or I figure it out myself. One good sign is I know have completely working dev/hack environments on OSX, win7, liveusb ubuntu AND linux mint debian so, I guess that is something.

YOU ARE NOT ALONE USBBOOT ONLY PEOPLE!! one love. =P