If you come across this alert, "The apk is not zipaligned. Please run the zipalign tool on the APK to improve performance", during your upload process to Google Play, it is likely that you are attempting to upload a debug .apk. The debug .apk is neither signed with a certificate nor is it optimised with the zipalign tool. If you are using Eclipse as you Android development IDE you will need to use the Android tools to create a release .apk. This will do all the necessary optimization required for a successful upload to Google Play (certification and zipalignment).
It worked for me and I hope it does for you