Just make sure you flash with the correct clockwork mod so the parition sizes are correct. It wouldn't hurt to go into CWM, format all the paritions (EXCEPT SDCARD) and try installing from zip again. See if that helps. I format all paritions every time I install a new version even though it's probably not 100% necessary...
Hope that helps. I'm running the latest version on my HD2 and it's stable despite a few minor bugs.