Help needed with Logic Pro X

I am working on a psychoacoustic project that requires me to edit very small bits of sine wave signal and then replicate it to usable lengths. I have been using Logic Pro 9 but recently upgraded to Logic Pro X (10.1.0) on a 64 bit Mac 4,1 (8 Core, 2.93 Gz, 36 G Mem.) running Yosemite (10.10). I now get pops as the playhead transitions from one region to the next. This didn't happen in Logic 9. All edits are snapped to 0! I've tried fades at the beginning and ending of each region but that doesn't seem to make much difference either.

I would appreciate any suggestions as to how to solve this. Product is meant to be used with headphones and the pops will totally destroy the effect. Thanks,