From the FMS FAQ :
FMS 2.0 Beta 7 won't install.
If the FMS installation displays this message: "There is already another version of FMS installed on this system. Please uninstall it first.", but you have uninstalled all old versions of the FMS you can do the following:
- Run RegEdit to edit your Windows registry
- Browse to the key "HKEY_CURRENT_USER\Software\Flying-Model-Simulator"
- Delete the whole folder "Flying-Model-Simulator" from the registry
- Try to install the FMS once more