I'm having the exact same problem but with different apps. I use RunKeeper, TomTom, and NavFree. All three apps have some GPS inaccuracies. I jog around a lake and RunKeeper has me running across the lake at some points of my route. TomTom and NavFree both report my live location to be on another street sometimes. As far as I can tell, it's random but other times it seems to happen at the exact same locations.
I have both the iphone 4 and 4s. This problem started upon updating my iphone 4 to ios 5. Prior to that, the GPS was very accurate in all of my routes. Both phones are now on ios 5.1.1 and this problem has persisted. I hope someone at Apple's reading this. There are dozens of threads about it already, yet no fix and ios 6 is already on the horizon.