Dez i think i've got to the bottom of it...!!!
When bouncing the trigger tracks, do you have any sends on the aux's with trigger inserted on them?
i had the kick trigger going to the snare triggers suppression sidechain and Vice Versa
This was all dandy in HD but for some reason REmoving the sends made the files line up properly in LE
This Is due to the aux i was sending having a delay and thus delaying the entire track!
it seemed to work without the suppression anyhow just thought id try it with a triggered signal so it was more reliable!