Okay so make sure this is unchecked first:
It sounds like it is, but just in case. Just above that check box-- Your Tool 1 (append) should say "wavtool.exe" and your Tool 2 (resample) should say "resampler.exe". These are your wavtool and your resampler, and they're the engine that drives UTAU. They control how it handles pitch and timing, among other things. You can download and use alternatives that change how things are processed. For now don't worry about it! Sometimes people just mess them up somehow, sowe ask about it because of that.
Is there any chance you can upload a screenshot of the render window if you can catch it? and a screenshot of the Voicebank Settings panel (under Tools > Voicebank settings, or ctrl+G)