I know there are fixes coming in the next point release that fix the MXF source media to EDL manager that have existed for a while. I am curious about your sequence. Can you send me a bin with the seqeunce to me at michael@24p.com
Record some LTC for that matches the record side timecode that you need to match. You can use Read Audio Timecode to get the timecode value, load it up, and make the edit or capture the V track with a timecode burn-in. Edit the LTC track onto the proper audio track and your done.