The tool doesn't overwrite any AFPD files so I'm not sure why it's crashing. Here are some questions for you.
1. Does it crash if you're flying in a regular AFPD scene and then try to switch to another one?
2. Which Reflex scenes exactly are you using? If you can provide a link, please do.
3. What does the crash do? System lockup? Illegal instruction dialog? App hang only?
4. Did you apply the latest AFPD patch?
5. Do you have the music feature enabled?
6. Are you now, or have you ever been, a member of the Communist party?
-Mark