To me that sounds like a field-domminance problem. If you are setting upper-first footage in a lower-first time-line, or the opposite, FC try to correct the difference in the field-domminance aplying a shift-fields filter to the clips in the time-line. The problem is that your KONA try to do the same so the fields order is chaged twice, and the result is wrong order. At least its happens like that with the Blackmagic cards. The solution (if is this the problem) is to uncheck the shift-field filter in the clips and the videocard will do it OK.
salud,
rafael