you're running multiple profiles of Firefox at the same time (so restarting one with a queued update writes the changes to disk, throwing the other profile instances out of alignment).
In that case, launching a different profile in a new window should not use the new version. In other words, Firefox should not do anything with the pending version until the user actually restarts the entire browser. Having the second window run in the new version just because there was a pending version seems like a bad approach.