After upgrading to Mac OS X Mavericks – I have had nothing but problems with Mail.app handling my Gmail accounts. I read that it might be addressed by making sure the “All Mail label is not hidden” – but that did not do anything for me. My message count is off, my message #s are not coming in correctly, my filters are not working, and I am pretty unhappy with what I am seeing.
Until we get a fix from Apple (hopefully soon!) – I have decided to fix my problems by just using good ol’ gmail (web). Let’s hope we get a Mac OS X 10.9 update soon!