A couple of things to check.
Are you presetting your time code? Make sure you’re laying some control track down (at least enough for preroll). Then set your TC generator to regen and assemble. I like to put down 30 seconds of black – 1 minute bars/tone – 20 seconds slate – 10 secs black or countdown. If your TC starts at 00:58:00:00, then your program will start at 1:00:00:00.
If you have a selection on your deck for LTC – VITC – AUTO, try selecting LTC.
Also check to make sure your TC generator is set to REC RUN and not FREE RUN.
Hope this helps.
FCP Studio 2
Dual 3Gg Quad Core
5Gg RAM
KONA 2
OS 10.4.11