There is a problem yes, but the problem is not with the new installer.
The problem appears to be with the code that launches the update installer and closes FlashFXP, I have made some changes to address this issue for the next build however since this problem is within FlashFXP you will not be able to see the fix until after you update from the fixed build.
I was not aware of this issue until you reported it, thank you for letting us know.
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