On our Kona SD system, as well as our Io systems, in order to digitize and have it remove the jitter frames creating 23.98 media, you have to do two things:
1) create a capture preset that has timebase as 23.98
2) digitize everything starting on an A frame (normally :00, :05:, :10, etc…)
We’re actually in the process of loading feature film dailies from Digitbeta, and digitizing to 23.98 fps DVCPRO-50. Working like a charm thus far.