I never found out what causes it, but updating to 6.0.3 has corrected the issue for me.
I'm on 6.0.3 but thanks for the response.
I suppose some other hardware/software details might be handy.
Windows 7 Pro with SP1
Premier Pro CS6 6.0.3
48 gigs RAM
AJA Kona 3
Anything else that might be useful to know?
Sorry, I just have no clue at all what might cause this behavior, and hence no clue on how to correct it.