First when you look at the capture_point entity, there is a couple things to understand.
There are these entries "X team must possed cap point" that are used to set up an capping order. Their use is quite straightforward. If CP B is after CP A, add, "CP_A" (or whatever name it has) in the CP B list.
But if you want a CP to be unlocked at any time you must add itself in the list, as only entry. If the point must be unlocked for both team, add itself both in Red Team must cap, and Blu team must cap, for instance.
Now, this doesn't make the CP unlocked. To be unlocked it must posses a corresponding trigger_capture_area entity, in active state. If you disable such an area, the corresponding CP will be considered locked by the game engine.
Maybe in your case, the issue is the game considers that capturing the unlocked CP counts as having all legit CPs. So check the things I've cited, and if all your CP have different Ids.