There is a known issue with variable mix (and some other things as well!) not always working properly when you mess with Pitch values, and what you describe sounds like it might be it. (And, unfortunately, there doesn't seem to be much I can do to fix it. That's just how RPG Maker's audio is.)
If you're using variable mix, you should always try to use 100 Pitch (or just don't set it; 100 is default.)
If you're not doing anything with Pitch values, then give me some example commands that you're using; both the load and the play commands.
PS. Oh, yes, and also check the lengths of the sound files. If track A is longer than track B and you mix from A to B, then it's possible you could be at a point in A that is past the end of B (relative to the tempo ratio, of course, if you're using that.)