Maybe the special energy thing was a safety precaution the "builders" built in? That sure worked well.
Well it did, They had almost wiped themselves out. From the grave the makers won. If you consider something like the Replicators form Star Gate, or the Borg, or those Robot Arms from Lexx... Only a fool doesn't believe in contingencies. It's possible that the Makers might have had trouble with machine life growing out of control earlier in their development, or just anticipated, or observed it happening to other advanced life forms putting their trust in AI that would eventually object to being enslaved... Not that was the problem here. Enemy AI killed opposing Makers to the death and vice versus, which is all above board.
Sorry, if I was creating a robot caste of warriors I'd include a redundancy called a self-destruct, off switch or something so if they start going apeshit, I can send a signal out to blow em all up, shut them all down. But what do I know?
Then your enemy hacks your system, breaks your cyphers and destroys your army using your own protocols