I would check out the Gate's website. Gates is the original manufacturer of the HTD, curvilinear timing belt series used by ducati. Here's a link to one of their troubleshooting PDF pages:
http://www.gates.com/facts/documents/Gf000287.pdf Look at page 4 of this document. Most likely what your experiencing is an angular misalignment issue.
I have not looked at your setup, and can't know for sure what kind of belt tension you're running, however, here's a blanket statement about synchronous timing belts: Increasing tension will not improve its ability to "track", it will however decrease the useful life of all drive system components. In fact, it's logical that a misalignment causing uneven wear will be exacerbated by increase loads (or tension) forcing the belt hard against the flange.
A timing belt is a compromise between a couple of issues. 1st there's durability, then there's the "timing" issue. Here's another blanket statement: More tension will enhance timing accuracy at the expense of durability. Obviously this isn't always true, just as running the belt "whip" loose will not increase durability. Gates recomments fitting a new synchronous belt approx. 25% tighter than a used one. If ducati doesn't have a spec in their manual for both new and used belts, I would have no idea what their tension spec means. Unless you own a frequency meter recommended by both Gates and Ducati, it is very difficult to manually set the tension "ideally" on the short-span, double idler drive setup found on the Ducati's.
As for myself, I check and adjust belt tension after every race weekend... and typically run it on the loose side, sacrificing a little timing accuracy, but knowing I'm not stretching the crap out of the belt as everything warms up and tension increases. On the old 2 valvers, people have been using the 5mm allen wrench trick with great success for many years... it even seems to work on the new DS motors. Not sure about the DesmoQuattro motor, but on the Testa motor, the idlers have flanges that make this trick difficult to pull-off.
As for fixing the issue? Whenever you buy a ducati, I recommend a complete disassembly of the motor to fix all of their mistakes. However, its possible that only the timing shaft bearings are cooked, unfortunately, you have to split the cases to change them. So, while you're in there anyway, you can fix all ducati's mistakes.
