What software are you using?
If you're using Makerware, I would try the same print in ReplicatorG to see if it changes. RepG is terrible software, but IMHO it's been better than Makerware. Especially if you don't mind getting your hands a little dirty with code. Like many here, I've switched to Simplify3D. It fixed 90% of my issues. Also there's this guide which can help, even if you're not using their software.