yeah, although it seems like creating a master frame in any program should yield the same results as in another, in practice trying to use master calibration frames from one program in another program rarely works right.
i think you should start from scratch with PI, using all of your flat,bias,dark subs and using PI to make the masters, if you want to do the calibration in PI.
the _r registered frames are actually rotated and translated (and perhaps scaled). if you open one you'll see some black areas that are due to the rotations and translations. but if the calibration has destroyed the data, then what's in the _r files is just junk.