In my case it does have an affect. I renamed my .htaccess in my forum root, then tried to access my admincp and pressed Cancel and it worked like it should, giving me a 404 error. When the .htaccess in my forum root is active and I press Cancel in admincp, it goes to the admincp login. The .htaccess password request keeps popping up after that, but eventually it goes away if I keep hitting Cancel. Either it has something to do with having an .htaccess file above the admincp .htaccess OR it is being affected by the VBSEO rewriting. I'll be looking into this further and let you know what I find out. Other opinions are welcome.
EDIT: I found that if you comment out the RewriteEngine On statement in the VBSEO .htaccess, the admincp .htaccess works as it should.