I experienced that too on my '96 900. It could be carb jetting or any number things.
You are most likely starved of fuel at that spot on the power band. It turned out, for me, that my fuel line had too tight a radius in it, and the hose kinked. I re-ran the line with a wider hose, and now it seem to have done the trick. I was lucky with the simplicity of the issue.
Often, if you have a custom exhaust and air filter replacement, the carb needs to be rejetted to account for the additional air.
Put the wideband in the pipe yesterday. From what I assume is stock jetting(PO) said he never touched anything. It was rich on idle - 12:1 and crazy lean WOT - 20:1 and backed down to 18:1 after a a bit, a touch rich partial throttle - 12:1
So I opened up the carb and put in a bigger main jet, got it down to about 12:1 at WOT, moved the clip on the needle and that brought idle up to 14:1, which is about right, didn't see a pilot jet and I was in a bit of a hurry so I left that alone. partial throttle is now about 12.5-13:1 with just the needle... which is close enough that I'll probably not mess with it, although I bet if I got that around 13-14:1 I'd get better gas milage without sacrificing any power.
Overall, it's like a whole new bike. No flat spot and 15 seat of the pants HP. And with 18:1 at WOT, I wouldn't be surprised if I actually gained 15hp. Even if this was not stock jetting, if someone else jetted this at some point they were retarded. The bike has been in MO and IL it's whole life so there is no excuse for a 18-20:1 a/f ratio at WOT except in an attempt to grenade the motor.