Heh, this is just easy to fix. Do what I'll say:
Open Folder where you have SRB2DB and delete srb2ex.cfg (unless you want to make 1.09.4 levels)
Open SRB2DB. And then Tools > Configuration > Files and then browse for srb2.srb in your SRB2 2.0 folder.
I think it will work then.
EDIT: Damn you, Fawfulfan