Lagging when shifting?? (727 auto, w/ full manual valve body)

Ok, well I did some tests of my own today, and what happens is there is a 2-5 second delay before the tranny shifts into 3rd(or drive). Now if I start off with the shifter in drive, it DOES shift by itself. And it does not do any sort of delay when being driven this way. However when manually shifted, it has a delay between 2nd and drive. Here are all the specs I know on the tranny:

A 727 that was rebuilt by Shift Management in Sacramento, CA, has Alto Racing Clutches, a dedicated TCI Trans Cooler, a 5.0:1 kickdown lever, a bolt in sprag(supposed to fix the weak link in the 727) and a 10" 3,000 Stall Hughes fully Brazed converter, and a supposed full manual valve body(which it obviously doesn't have).