That's exactly why i fear installing this app. Try to push your mac at the max so that the fans would normally kick in. (something well over 20%)For some reason my fans don't adjust themselves when I dont have SMC on. Or maybe it's because I havent even gotten my usage over 20% yet or something. But i've reached 140 degrees and though that they would adjust
I found a solution for you if (i hope not) the fans stay at 2000 RPM all the time. It's called resetting the SMC.
Let me know if it helped you...
EDIT: Just found this... However in order not to damage your machine scFanControl let's you not set minimum speed to a rate under Apple's defaults. In addition to that fans are still in automatic mode, so the speed of your fans will increase, if CPU load gets higher. I think this is what you're dealing with right? Did you use smc fancontrol 2.1 (or 2.1.2) or an earlier version?