I had the same issues with USB devices not being recognized unless they were plugged in at boot. As mentioned in the posts above, a mismatch in version numbers seems to be the most common cause. I found the below post over on InsanelyMac Forums extremely helpful with instructions on how to diagnose whether a mismatch in version numbers is the problem and also how to correct the problem with files provided.

http://forum.insanelymac.com/index.php?showtopic=95789

This was posted in March and there may be a more up to date fix. Most of the people experiencing the problem had installed Kalyway's 10.5.2. AMD which by default installs 9.2.0 Sleep Kernel & 9.2.2 system.kext.

Good luck