You might want to verify the setup in the VM and make sure the changes you make are being saved. Since you repackaged FlashFXP did this include removing the installer, if so perhaps the proper configuration isn't being set in your installer.
The details section of the [proxy] is hidden using a a random bit shifting xor encryption.
If you create a master flashfxp.ini with your tailored settings and then use it as part of the install process it should work without any problems.
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