I don't claim to be very ducati-tech knowledgable but if you have the same clutch system as my 2000 750 you may have a leaky clutch slave cylinder. If the slave leaks oil, you will lose pressure in your clutch lever and therefore cannot totally disengage your gears. Same thing happened to me - it got worse and worse until i realized what was happening.. Its also bad on the gears to be shifting when you are not totally disengaging each gear between shifts.
Anyways, solution: install a new clutch slave cylinder. I purchased a Yoyodyne for around $200. A slightly lower cost option is the Evoluzione slave. Both seem to get pretty favorable reviews.
Hopefully thats the problem.