It's a strange situation, I do not know if I solve it.
What I think :
==> Use SRB2 Doom Builder rather than the classical Doom Builder.
==> Then you do NOT have to delete files when you downloaded SRB2 DB, because you think they are useless, but they are files that run the application (. dll files, mostly).
==> My last proposal : You should store all files for Sonic Robo Blast 2 in a folder. Then, in this case, I suggest you put MY SRB2 Doom Builder with MY configurations that works.
In my archive, there is a folder. You just place this folder in your SRB2 folder.
However, you must configure some things !
Tools ==> Configuration ==> Files Tab ==> Click on SRB2 v2.0, and then Browse ... and seek your IWAD (so srb2.srb).
And last thing ...
When you create a new map ...
Do not forget to configure on SRB2 v2.0!
Good luck. If it does not work, I can not anymore.
My SRB2DB download :
http://www.mediafire.com/?3k3nejmurx10dek