Hi, I am just stumbling on your posting, but we had been having this same problem and we thought it was the Kona 3 card.
what we did find was that our digitizer was noot locking onto the AJa presets we set up and the kona kept switching back to Free run in the Control panel… whenever a drift like that occurs, especially gradually, it typically means there is a Ref In/timing problem.
check your playback timeing setup in your AJA control panel and make sure you have Ref In genlock – Locked.
that may help.
I did some tests on our side and we have seen an improvement so far.
Colleen