What I'd like to understand is whether I'm better off using BWPs on its own...
Update: That is actually what I ended up doing, but I cannot now remember where I had read something somewhere about BulletProof and WordPress 3.5 not being well-suited for each other. However, I do know (from at least my own experience) you can either tell BulletProof to restore the default files or else just do that manually (FTP, like I did) and then BulletProof will be back at Step One...and you can decide from there.