Some water companies will give you some credit against charges that obviously resulted from a leak. It's worth calling them and pleading your case, especially since you probably would have found the leak earlier if they'd read the meter. The worst thing they can do is say "no." It's also worth checking the meter yourself against your bill to make sure they didn't mis-read it. Even over 3 months, $1,000 worth of water in the midwest is a hell of a lot of water.
Fix the leak first, though. Based on your description of the "running" softener, it seems likely that you've found the source of the problem. I hope it's as simple as that and not an underground or underslab leak somewhere. Good luck!