Actually, the "new version is worse than the old" is true for some sequences and not for others. Obviously you've hit a sequence (or more than one) where the tracking is worse.
We will be coming out with a new version soon that will allow you to select the "old" versus the "new" tracking (you'll want to use the one that works best for a particular sequence). Until then we can give you a version 2 key if you don't already have one, so that you can get the current sequence rendered properly (simply write to us at firstname.lastname@example.org).
Bottom line: we know that the new tracking doesn't work better in all cases, so we will be providing an option to switch between the two trackers in an upcoming update (the update will be free to version 3 users).