Well, I haven't replied for a couple of reasons. First off, I was on vacation for a few weeks. Second, I've always asked that admins post their questions in a new thread, rather than tacking on to this one. That way, if someone else has the same question, or the answer, they are more likely to see the post.
DSpawn: I'd want to see your command line and perhaps your startup spam to get a better idea what the problem was. I'd recommend you use seta instead of set for everything except map rotation items--that includes putting seta in front of rconpassword.
Revan Bakr': The server.cfg file belongs in the base directory, along with the pk3 files. When you ask, "how do I include the coding inside?" what do you mean? If you mean, how do I get the server to use the config, you put +exec server.cfg at the end of your command line/shortcut. If you mean, what types of things should/can you put in the config, that's a bit more lengthly answer and I'd want to make sure that was the case before I went on and on about it.
"Do you expect me to talk?"
"No, Mr. Bond, I expect you to DIE."