Seeing as how they were going to charge you so much for labor on your supplied parts I wouldnt put it past them to just tell you that the driveshaft was offcentered even if it wasn't, just so you'd have to spend more money.
About the filters. The filter inside of the transmission itself is never supposed to be changed, it's supposedly good for the life of the transmission. The external filter however should be replaced every 30k or whatever the manual recommends.