I'm having the same issue on and XP SP3 box after upgrading my AMD (ATI) graphic drivers. Uninstalled and reinstalled boinc to no avail.

On windows there's only 2 disk locations where files are: The program files directory and the data directory [from 6.x clients]. The pieces remembered are in the system registry such as windows location and size. Not recommending to mess with that unless you know what you're doing. Operational settings [how what where when to crunch] are not stored there. Of course, if you did clean out entirely to include the special limited rights BOINC accounts, then booting and installing and booting again is a requirement before BOINC can function again in protected application execution (service) mode.

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edit: As for ZoSo's ''su'', I'd never run this way in elevated rights session. "sudo" to executed something with admin/root rights is the recommended operation so for instance "sudo service boinc-client start" [or stop] would be the way to launch/halt the core client daemon. After issuing a sudo all admin requiring commands in the current terminal session do not require to enter your password for [IIRC] 30 minutes default, but [re]using sudo makes you aware that you're executing with elevated rights i.e. if next you do i.e. a chmod without sudo it will tell you "permission denied". You will be reminded that [big] damage can be caused in terminal.