From MacbookPro to MacPro latency, Sessions out of sync.

Moving from a MacbookPro to a MacPro and loading up a session, I was rudely surprised.
On the MacPro the multiple kick/snare/hihat layers are all out of phase, When they were perfectly in phase on the MacbookPro.
All instruments had plugins on them and the MacPro can proccess them alot faster.
Is there any way to fix this, some sort of compensation checkbox in settings somewhere?.
Or should I just re-aligning them all?

If anyone is interested this seemed to be a problem with prores. When I use a AIC file and conform from 25 to 23.98 then it works fine.

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