You may have already done this, but I didn't realize that I was backing up my Lotus Notes databases twice when I first started using BE. When backing up the drive that holds your Lotus Notes databases, you should exclude *.nsf \subdir. Then make sure that your databases are selected in the Lotus Domino Databases section.
In my case the drive that holds my Lotus Notes databases is backed up at 458 MB/Min (3.4GB not including any databases) and the Lotus Domino Databases is backed up at 1,187 MB/Min (29.8GB only databases).
Hope this helps.