Holo, your post really confuses me, so bear with me if I ask some stupid questions or suggest things that are just wrong while I try to understand what you mean.
First, my initial read on what you wrote was that perhaps you are talking about the color of the bases on the D2 hex map. For as long as I can remember, bases (and planets) would retain whatever color they had when you logged in until you next logged out and restarted (or simply logged back in perhaps -- don't recall). This was a display issue only, and was not an indicator of base or planet ownership. This is one of those bugs that don't hurt the function of the game, but are sort of annoying on a recurring basis. If this is not what you were describing, please disregard.
Second, if you are actually having trouble in OP getting bases to flip to your control, where is the problem occurring? You indicate you are able to take the hexes. I'm assuming that this means the political settings and cartel layer interaction are set up in such a way as to allow you to actually take and hold hexes. If you're taking them, then there should be no problem with bases acting as supply points and shipyards once you own the hex. Again, I think maybe the color issue is causing some confusion. Outside of that, I'd need more information before I could really say what's going on.