Strange sequencin problems

I was trying to play in and this splice parts of a guitar riff and then sequence them. Basically it came down to an intro, a body a chorus and an outro. So I recorded the riff in, spliced the parts, did a tempo detect on each and the time stretched them to meet the same tempo. If I take one of the samples and play it in a loop you can see tell my sample cut points are right. But when I try to enter them in a sequence there are gaps at points that they just dont exist in. Also I tried dropping in a note/sample in front of some others and it completely stop play of the following note events.


Bizarre.