Keep in mind if a clip is "relative", it will base it's start transformations on the previous clip. This is where your problems most likely are. You need to decide on you chracter which channels are relative, and which are absolute. For example, if it's a walk sequence, the body's forward motion is probably relative (you want it based on the last clip played), but all the other rotational channels you want absolute. You'll have to build your character sets accordingly.
In general, I stay away from Trax, I've never heard of someone using it with good results.