Does this happen on any QVW files you reloaded? or only with a certain file? Also, if somebody else logging in with another account, does he/she also experience the same thing?
If you only have 1 file now and it's behaving this way, I would suggest you created a new QVW and simply use an LOAD INLINE to create 1-2 dummy records. Place this file into your "Source Document" and reload/distribute it to yourself. Now see both on opening the file directly and via AccessPoint whether it shows the same data or not.
On this file, do you have Section Access logic? If not, would you check as what Hampus suggested, which is check how "Reduce" option is being setup for that QVW (A screenshot would be nice so that others can see whether there's something is not set properly).