Re: File Edit
Which specific build are you using?
Do you recall what build you upgraded from?
Were the files edited remotely or were they edited locally using the "edit and upload" feature? I suspect that you were.
By default FlashFXP will remember your edit history and reload it on connect, If you used the "edit and upload" feature then FlashFXP will check to see if the local file has been modified since the last time it was uploaded, if it has then FlashFXP will trigger the "default action".
You can configure FlashFXP to not remember the edit history via the Preferences > View and Edit File.