I can't tell you why it did work and now it doesn't, but I can tell you how to tweak it so it works again.
First go to Audio/Video settings (Command-Option-Q).
Find the Device Control Tab
Find the preset you are using, AJA Kona2: 29.97 Sony VTR B Device Control Preset
Duplicate it.
Edit the Duplicate
Near the bottom of the pane that opens, adjust playback offset to suit.
-V