Ok,
I’ve had a reply from Rudy at AJA. It appears to be a settings issue. Here are his instructions:
1) Go to AJA control panel -> format:
a) Set the Primary to 525i23.98.
b) Set the Secondary to 1080pSF23.98.
2) Setup FCP with a AJA Kona 3 NTSC 23.98 easy setup.
3) Go to FCP audio video settings and set the device control preset to AJA
Kona 3 23.98 Sony VTR A. This should get you 23.98 timecode.
4) Go to FCP audio video settings -> capture presets(tab) and click on
(this will put you in the capture preset editor and you will be
editing the copy).
a) Set the Input to AJA Kona 525i23.98 (720×486).
b) Rename the capture preset accordingly and save.
The difference between the original 525i23.98 capture preset and then one
you have created is this: The original capture presets looks for a 525i29.97
input signal and remove 3:2 pull-down. The new capture preset looks for a
525i23.98 video signal and does not remove 3:2 pull-down. The frame buffer
should now show 525i23.98 on capture.
I’ve done this and can confirm that it works!!!
Thanks to everyone who helped sort it out.
Andrij