Reuben,
There may be an important piece of information on the process that we are missing here. Frankly, your description of the situation and the resulting problem doesn't quite make sense. I'm not saying it's your fault, I'm just saying that something seems to be missing from the equation.
Are all the tracks sped up by the exact same buck-forty rate, or is there a sync problem between the tracks even before you try the pitch shift?
If they drift out of sync - even by a less noticable amount - before you apply the pitch shift, the the tracks left the studio out of sync. This is probably the case as I can see no reason why tracks that are perfectly in sync would suddenly drift out of sync if the identical pitch shift is applied to all of them evenly.
If they are indeed perfectly in sync before the pitch shift, then you might wantto double check that you applied the pitch shift evenly to all the tracks (e.g. that the shift was applied to the entire length of each track and that the amount of shift was identical.)
If they are indeed slightly out of sync before the pitch shift is applied, then you need to contact the studio and see what's up. Were they out of sync before hitting the Fostex? If so, was there a problem with the source files? How were the source files recorded and compiled? if they were transferred or compiled digitally and without a master clock source, drifting could and probably would have occoured at that point.
And even if there were such sync problems with the source, why the $1.40 speed up? Did the studio do that to try and mask the sync problem, or did they do that under someone else's instruction?
I think the only real chance you have to find the answers to these questions is to backtrack the chain of evidence (so to speak.) The only way to do that is to call the studio and see what they have to say about it.
G.