Hi, soens. It's been a while so I'm not sure if this is exactly the issue you are having but it sure sounds like it. Google the forum for a thread by FastBikerBoy (Karl) about Audiosnap. He did a couple vids last year about this issue. You have to fiddle with the beats at the start of the timeline before it will accept certain beat/tempo setups. It's kind of finicky and a PITA but it works.
Edit: See post #5. I found the vids.
Google: Cakewalk Forums + FastBikerBoy + Audiosnap + vids or videos.
Or you could just check his youtube page. They were there last time I checked.
After watching the Anderton Berklee vid I noticed the AS timeline stuff looked different in X3. I'm not certain and I haven't tried it yet (too busy with other crap) nor have I seen any mention of a feature update in that area but it did look a heck of a lot sleeker than I remember. I also mentioned to Bill a while back about Audiosnap 3.0 because it really could use some improvements. He seemed to like the idea and said maybe they'd look into it. One can only hope.
Good luck.