When upgrading to FlashFXP v3.6 we recommend storing your data files in the user application data folder. The problem with storing the data file else where is that your user account doesn't have write access to save the changes.
In the next RC release we will be including more warnings about this behavior.
Using the administrator account you can give your user account the proper file permissions for the files located in C:\ProgramData\FlashFXP\3\
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