Sorry for the lack of info to begin with, it was late at night when I posted
I am running Windows 7 x64 with no anti-virus. I'll put MSSE on eventually just not got round to it yet.
When the installer began, FlashFXP window dissapeared like it was killed for the upgrade. I didn't check it was still in task manager.
I did attempt a few times on the night I made the video, using Acronis True Image to restore the PC each time it failed. However since then, I have uninstalled, manually removed the folder and re-installed using FlashFXP41_1658_Setup.exe, so I can't now reproduce the error.
Guess it'll just have to be one of those things.