I saw a particularly good post from Bob Zelin on FCP-L about trashing preferences and resetting FCP, especially if you are having difficulty with an AJA card:
Trash your preferences. You must do this "all the way".
This is how to delete the Final Cut Pro preferences:
Quit Final Cut Pro.
on your MAC internal hard drive, navigate to /users/yourloginname/library/preferences, and delete this file - com.apple.FinalCutPro.plist
and delete these three files -
Final Cut Pro 6.0 Preferences
Final Cut Pro Obj Cache
Final Cut Pro Prof Cache
thats is ! Relaunch Final Cut Pro, and you will be "starting from scratch".
Now, launch FCP. Right away, to to EASY SETUPS. Choose an EASY SETUP that relates to the AJA Kona LHi drivers, not 8 bit uncompressed or DV/NTSC, or something like that. Choose something like AJA Kona NTSC 8 bit uncompressed, etc. OK, now CREATE A NEW SEQUENCE (file>new sequence), and click on this new sequence. Try to open up color bars on your timeline from the film strip. Do you see color bars ? Is it on your TV ? Go to VIEW>EXTERNAL VIDEO>ALL FRAMES. Is it on your TV ?
If the answer is still NO, then your FCP install is corrupt and you must reinstall FCP.
Of course--you follow this at your own risk and if you toss the wrong file its your responsibility. However, I've done this before with positive results.