I figured it out, guys. Following a suggestion that someone gave me in one of the forums that I post on, I changed the location where the map is created. (The person suggested this as a note with a nother problem I had a while ago, so I guessed that It could have been contributing.) Basically all I did was change the location from half-life/tfc/maps folder to hammer/maps folderr. After the compilation I just moved the bsp, but for some reason that actually caused the problem. So I just changed the settings back and now it's fine.
BTW, I did go to tfcmapper to help me set up the goals, and (my map kinda being a mixture of a 2fort and a dustbowl style map) I configured my map as a mixture of the two.
Was there anything that you noticed that stuck out when you looked at the map, Andy?
Because when I play the map the points and flag system work the way I want them to, but considering how complicated the entities, especially goal entities, can get, I'm sure I missed something.
-panda