i don't think its related to the s3tc textures, as i have that issue alot even though i don't have the s3tc textures installed on my current setup.
i'm assuming you're using 227 right? does the mover still show up fine in ued after saving and playing the map? (eg in mover->show poly's?)
i think some of the implentation of ued2 is a bit screwy in 227, i've found it doing a "transform permanently" on alot of my movers, therefore misaligning their textures... it would have been a seriously annoying issue if it werent for ued2's mover->show poly's feature