When you install, are you also reinstalling the Google Apps .zip file?
In other words, with GSB, if you are going to try to flash an update without doing a wipe data/factory reset, to try to preserve apps and settings, the steps should be:
- Restart in Recovery
- [optional] Nandroid backup (just in case - always good to do)
- [optional] wipe Dalvik cache - Amon's Recovery doesn't seem to do this properly, from what I can see, but it won't hurt
- flash the new GSB .zip file
- flash the gapps .zip file
- restart the phone
The reason for this is that the flash of GSB will wipe the current contents of the /system internal partition, so you have to flash Google apps again to put those Google parts back in /system
If you are already doing this, then I'm not sure what you are doing wrong. With the exception of 1.8.1, which I never installed, I have been able to flash a new version over using that procedure.