As you may or may not know, the SPC playback core used in ZC is pretty shoddy. The off-key pitch balance seems to be correct now, but the fact remains that it's still a little... slow to respond. That leaves you with notes which last a split second longer than they really should.
Now maybe it's just slow code... Or perhaps it's not reading instructions correctly. Take a look at any of the output you get from OpenSPC in a Tracker editor, for instance. Notice the fact that when a note should be cut off, what it's really trying to do is slide the volume instead? Putting a "note cut" where the volume slide begins will fix it.
Well, seeing as how SPC instructions are laid out a lot like Tracker instructions in most cases, it might be logical to assume that the playback core is doing the same thing: Slide the volume to the new value instead of instantaneously switching like it's supposed to. (Legitimate volume slides, by the way, are accomplished by a different kind of command.)
Granted, this is a shot in the dark, and it may not even work, but it could use some looking into.