I had this problem too… did everything right per the instructions — but I solved it! I was upgrading from a version (1.0b1) where the structure was mainly in the mu-plugins folder. After upgrading database must have still pointed to that location, and so after I deleted the buddypress files in mu-plugins, it gave me the error message.
All I did to solve it was go to Buddypress -> General Settings and selected the skeleton BP theme, saved settings, then selected the default BP theme, saved settings. I assume that fixed the entry in the database.
