And I merged two of your threads about this problem and deleted the 3rd. ;)
I don't know what causes this issue, my guess would have been that no write permissions were set or Vista's file virtualization is causing it, but you probably checked that already.
Anyway, as a temporary workaround until the solution has been found you can manually edit the options.lua file to adjust your gameplay and graphics/audio settings, just compare the entries with the options screen to find out what is what. The file can be found here: \Eagle Dynamics\Ka-50\BlackShark\data\scripts. Do not use Windows notepad to edit it, but a good editor like Notepad++. In order to map joystick buttons you will have to use your profiling software, the only issue that may remain is if BS assigns the wrong joystick axises.