Does this happen with all cloaked ships with cloak boosting in human hands, or only eye-bots? If it all such ships, then there may be a weird bug lingering with the cloak boosting through wormhole change. If it is only the eye-bots, then that would be a REALLY weird bug.
I know this is a somewhat obvious question, but are you making sure to put the eye-bots in low power mode before sending them to whatever, so they don't decloak themselves instantly by firing?