Can you give us specifics about what you're doing - your complete workflow, in other words?
Do you possibly have edits/fades on EA enabled real-time tracks? If so, that could be the problem.
Which algorithm are you using (other than X-Form)?
If you do a search for elastic audio, I've made several posts about how to get the best results. Yours are not normal and it's quite likely there's something in the method you're using that's causing the problem - but we'll need to know specifics to determine what it may be. Have a video capture would be even better - you can use the free
Jing software to create and upload a video.