Without making things overly complicated because this is a very complicated situation let me try to make it simple.
All versions prior to v3.6 were not intended for windows Vista and because of this upgrading from them to v3.6 is not as easy as it should be, and due to the way Vista security works there is no way for us to make it any easier.
The best way to install FlashFXP v3.6 on Vista is to follow these steps.
1. Run FlashFXP, From the main menu > Tools > Backup/Restore Configuration > Backup, and save your settings in a safe place.
2. Uninstall your previous version of FlashFXP, during uninstall it will ask you to remove your data files, for sanity I'd recommend you say no, just in case you goofed step 1.
3. Install FlashFXP v3.6, since this is a new install everything should default to the correct settings.
4. Run FlashFXP and restore the backup you created in step 1.
On Vista all installers run as administrator with full access, since the installer has full access it can't verify to make sure each individual user account also has write access to the same folders.
This is why the biggest issue for people upgrading is that their data files won't save, the installer is using a location that doesn't give the user write access. To remedy this you need to re-run the installer and do a custom install and make sure the data folder is pointing to a location where you can modify files.
Second of course is the fact that since now the data folder has changed FlashFXP can't find your old data.
Since FlashFXP is now Vista ready and no longer runs in compatibility mode it no can't even access to your old data folder which was probably in some virtualstore which ironically can only be accessed with administrator access or programs running in compatibility mode.
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