OK here goes for some answers,

"You're not joining the 3 AC3 files together and trying to sync the whole file that way are you?"
no I am not joining the files first,only doing 1 side at a time,I think if I join them all now and try the whole thing at once it would be that much further out.

"What prog are you using to decode/downmix the AC3?"
I usually use PX3's AC3 to WAV but thought that my be the problem so then I tried BeSweet,and same results with both.

Thanks again for trying to help me sort this out,I will try Vegas and see what happens.