I would make sure VITC switch is on, so that it is being recorded. Then I would set timecode to internal, set the start time of the deck’s tc generator to the time near what your sequence uses, and black a minute or so. Then you can switch the TC display (via menu?) between VITC and LTC and play back this section to make sure the two timecodes match.
Then I’d switch the TC to regenerate, and use edit to tape from FCP. The serial control should locate the timecode on the tape that matches your sequence, then sync the internal TC generator to match as it inserts video and audio and both types of timecode through the rest of the blacked portion and continues through the unblacked portion to the end of your show.
I don’t have that particulary deck, but this method has worked on other Sony models.
Perhaps now you’re not writing any VITC, so you’re getting old VITC that was on the source video.