I just got mine going and ran into a few similar issues. I had everything working and then next time I started my machine and went into a table and opened BAM neither camera was showing up. So I exited and ran the PS3Eye test program and it wasn't seeing a camera either. A reboot didn't fix it so I uninstalled and reinstalled the driver and that fixed things.
Then I had another time where when I went into BAM I had no cameras but when I exited and checked the PS3Eye test was showing the camera working. Fully exiting and restarting FP/BAM fixed that occurence.
I've also had BAM lockup when I exit calibration and try to reenter it. Ususally this is when I'm trying to get a better quality number. It doesn't seem to like me going back to previous menu and going back into calibration if I stop before doing the 3 dots part of the calibration.
I have my cabinet wired with a switch that removes all power and a button wired into the normal pc on/off button. So the way I shutdown is I press the button and Windows will exit and do a shutdown leaving my TV powered and then I flip the switch which turns everything else off.
By the way I made my own camera mods, cal board, and glasses but I got advice from Ranr when things weren't working well and he got me straightened out so much appreciation to Randr for his help.