while you are there, see if skynet disables the security when you have him fixed up, in my save, he doesn't drop the forcefields or disable any of the other robots if they are still active, but I also did the same thing as you, and thought that the forcefields might have dropped,
[spoiler:9128023aee]
I originally flipped the switch (off) outside of the base, where the generators are, (manhole) but that makes it harder to move around, and a bit pointless as well, as the forcefields eat into your health whenever you go through them, best not to go there, and have the forcefields at full power, but you need a decent repair skill or vic in your party, other thing is, if you fail too many times it will activate the security bots, so save before you deactivate the emitters[/spoiler:9128023aee]
but yeah, I do think the base could be a bit bugged, (and maybe skynet's combat settings could be modified when you first get him, or maybe dependent on the brain you get him? as I got him the cyber brain, he should have had melee then range, or maybe just range, also in combat he stays where he is, that makes him useless, that should be, stay close to me, or another option, (at least with the cyber brain) not checked his options with other brains,