mpc 1000 sequencer problem

ok so i have the mpc 1000 slaved to pro tools with MTC (using jjos) my problem is this. it syncs when im in sequence mode but what i have done is put two blank bars on sequence 1 and my tracks on sequence two, three etc so when i switch to song mode to track out i press play on pro tools and the mpc skips to the end of all of the sequences?! am i missing something here and doing something wrong? when i remain in sequence mode it syncs up without skipping but i dont have the two bars pre roll so the sync is very innacurate.. please me advise me on what im doing wrong if anyting.
if i have been unclear in what is happening just let me know and i will try to re explain
cheers

so basically to put it simply,
when synced to pro tools in song mode it skips to the end of all sequences...
can anyone help me out here?

MTC syncs the playback position to the exact time, so only thing i could imagine is that you are not starting protools from the beginning of the song...