I had a bit of a prob with my 900ssie last summer, sometimes when started it would feel and sound like it was running on 1 cylinder, popping and banging and blowing loads a black smoke on revving, when ridden it was hard to ride normally but only when given a fistful it ride normal again until i backed off.
Not sure if they are the same symptoms you are suffering with???
Although after several mechanics had a look, and new leads, plugs, injectors, filters e.t.c. took her to ducati to be plugged on a diagnostic machine, to find out it was the cold start valve that was f**ked, and it was tricking the ECU to thinking the engine was cold, and fuelling to make up for it.
.
Oh well live and learn.!!!!
Hope that is of some help m8.
Steve