When Evernote is not running (completely not running, make sure no hidden tasks got stuck by using Task Manager), use regedit and manually change HKCU/Software/Evernote/Evernote/EvernotePath (REG_SZ) to point the path you want. It sounds like somehow that value isn't being flushed to the registry.
(If that value is not set, the default is your <user profile>\Evernote\Evernote.)