SnoBrdr
With the new auto install via LiveUpdate some users were experiencing auto reboots as well. Which is not what we wanted to do.
So several builds ago I changed the flag "NoReboot" in the installer to true that basically instructs the installer to never reboot the computer regardless of the situation.
If for whatever reason the installer is unable to replace a file because its in use it will not complete the installation until the computer is manually rebooted.
The installer is supposed to do a check to make sure that FlashFXP isn't already running before continuing, if it is running it should display a prompt.
I did some quick tests and I can confirm that this check does appear to be working and will prevent installation until FlashFXP is closed.
What version of Windows are you using?
Can you please send me a copy of the following two files from your FlashFXP program folder.