I just ran a test on Fx 16.0.2, temp-allowing a site, closed, restart, and the temp permission was properly revoked.
You could double-check in
Windows Task Manager (Ctrl+Alt+Del) > Processes that all instances of firefox.exe have been terminated.
Mozilla has recommended closing Firefox by using File > Exit in this situation rather than the X box in the upper right, though I've never found it to be necessary.
If none of these help, then yes, an extension conflict is quite possible, so please follow Thrawn's advice about a clean profile with NoScript only.
If that solves the problem, you can narrow down the problem extension with
Standard Diagnostic, or just pair each of your other add-ons, one at a time, with NS, until the culprit is found. Let us know, thanks.