[Fyron]

Were you wanting a map with no warp points, or disjoint clusters? There are two different settings, which have radically different affects. No Warp Points naturally supercedes Not All Warp Points Connected.

Not All Warp Points Connected tends to produce fairly random distributions of what is connected and what is not, so it is not surprising to see the occasional map with one huge chunk of the galaxy connected and several small bits of just a few systems.

You can see what technology the AI has developed by going to the Options menu, then clicking on Players. Toggle off AI control for a particular empire. After you hit end turn, it will load up their empire as if it were a human controlled empire. Normally this is cheating, but since you just want to see how they are creating the warp points, it is fine. The AIs have settings to research Stellar Manipulation far earlier in "Not Connected" states, which translates to "Can not meet other empires due to being cut off into a small portion of the galaxy."