I'm guessing, but I think that most of the BES guys here are on Exchange systems (I am), so we can't really help with a Domino/Notes configuration... Sorry
I recently encountered this problem on my PC, it happened when I installed notes onto another partition (F drive) then installed it back on my (C drive), this seemed to screw the notes.ini file.
To solve the problem I completely removed Lotus Notes and BBDM, then re-installed everything. Worked fine afterwards.
Check Lotus Notes hasn't been installed in two different locations.
Or as a quick fix you may want to manually specify the location of the Notes.ini file before you login using the Advanced Button.