I've been using flashed version since the eeprom implementations a month or so ago and had no issues until recently when I copied the .rockbox folder and iriver.rockbox files over using the bootloader usb mode.
On removing from usb it continued to boot OK, but when i tried to flash the iriver.rockbox file it returned an incompatable version message. (note music playback was still fine, just unable to run any plugins). This presumably is because the plugin version was bumped and the new files in the .rockbox folder were not operating in conjuction with the older iriver.rockbox file installed and operating from the flash.
I had to reload the older versions files and reflash the newer version after loading the firmware then using the normal bootloader (ie. non usb bootloader).
I just wanted to point this out incase anyone encounters the same problem, and to raise awareness of this potential issue (i don't think it's been mentioned before).