Three rules of waittime:
1. If the sucker tube has a speed and a waittime, that many seconds will pass upon entering the tube tile before leaving the tube tile.
2. Rule 1 is true UNLESS the sucker tube event with the waittime is the last sucker tube tile you used (no matter how long it's been), in which case the waittime will be ignored. The use of any other sucker tube anywhere in the level, waittimed or not, will cancel this.
3. If you land on a suckertube with waittime while in the falling-from-a-warp-target mode, prior to entering any other sucker tube, and there is no ground tile underneath the waittimed sucker tube, you will get stuck. This is probably your issue?