I went through the source code and I discovered an ini only setting that lets you turn off the dynamic menu. By turning it off FlashFXP will use more system resources. With it off you will be able to use Ctrl-S like you did in previous versions.
1. Close FlashFXP
2. open the flashfxp.ini in notepad
3. add the line "DynamicMenu=1" under the "[main]" section (without the quotes)
4. save flashfxp.ini
5. start FlashFXP
Once we start disallowing custom commands to use the same shortcut keys as defined in FlashFXP you will need to find another key combination regardless of using this above mentioned solution.
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