I've never experienced anything like that. I've made probably a hundred CD's (from mp3's and AIFF's) taken from concerts, etc., that demand a seamless changing of tracks, and it's worked perfectly everytime. I've even downloaded mp3's from various sources that are meant to go together, and when I burn it, perfect again. I've done this with the free Toast and now Toast Titanium on my Zip650. (I've not tried it with Disk Burner because I don't have one on my beast.)
Again...I realise that there is nothing here that can help you, except to say that in my experience the burner has done exactly what it said it would do.
The only thing I can think of is that the source mp3's might have a bit of dead space at the begining of them...but I can't see that happening every time.
Perhaps if you extracted the audio from a commercial CD that has seamless tracking, and then tried burning it youself from the extracted tracks to see if the noticable gaps are still there. You wouldn't have to do the whole thing, just a few tracks.
[edit] You say that you first noticed this when you burnt a cd with mp3's from a continuous mix. Perhaps the source cd did a tiny bit of cross-fading between the tracks. If you didn't burn them in the same order, then you would certainly notice a shift in the tracking.