It has been 6 years since I did anything with Acid but here's what I remember. Your stems will need to be "acidized" when brought in. You can go into properties on each stem and define if it is a loop, a non-loop element, or a beatmapped file. And the key will need to be set. Otherwise your stems will all be processed at whatever the default BPM tempo is of your project. Which IIRC is 120BPM unless you change project tempo. A quick fix, if all the stems appear to be off at the same tempo, which they probably are since they were exported from ProTools, might be simply to adjust the project tempo.