This might be blatantly obvious to someone else, but could you first tell us what year your bike is?
I had similar issues with my '95 900ss which turned out to be the carburetor. I had to do a full tear-down, cleaning of the carbs, and recalibration to fix it. If it is indeed the carbs, you may have a obstructed main jet. Aside from the RPMs, does the jerkiness also have anything to do with how open the throttle is? If it happens on multiple gears at/around the same throttle position it's probably the carbs.
However, if your SS is fuel injected, what I just said doesn't apply.
Also, anecdotally, I had a friend with a 900M who's ride was jerky (she described it as 'angry') which turned out to be a cracked head gasket.
Anyway, if you can provide a little more info (about your bike and exactly how/when your problems happen), I'm sure the great folks here can give you more help than I ever could.
