I have always wondered what happened to the others like Ruk
Were there others like Ruk?
Note that the installation has doorways shaped to fit the Krell species, rather than ones suited for humanoids like Ruk, and all furniture suited for humans appears cobbled together. Perhaps the Old Ones were actually giant crabs, and their servant robots were accordingly shaped. "Ruk" may have been what the machines spat out when they realized that a new master, now shaped like Korby, was in need of robotic services. It's just the servant's latest body, many of the former ones having been crab-shaped.
Ruk actually being an entity residing in the installation's mainframe most of the time would also make it natural for him to locate and assist Korby originally: he'd have ears and eyes everywhere, waiting for masters in need, and would only develop a pair of helping hands when needed. Although we don't need to assume Korby was found outside; rather, his survival may be due to him finding his way inside the installation first.
The protection order doesn't seem to come up until Korby programs him to protect his experiments.
Good point. And while the Old Ones may have died exactly because their servants became overeager as guardians, Ruk thereafter may have lost his appetite for guarding and developed a yearning for servitude, that is, companionship. He does have the ability to flexibly reprogram and reprioritize himself; he only struggles with circumventing direct orders.
I'm still a bit unconvinced that Korby did to himself (or had Ruk do to himself) what he did to Kirk. That is, Kirk got "synthetic organs" while Korby got "direct transfer (of mind and soul)" - but it doesn't appear that the opposite would be true, as the copy of Kirk was programmed and reputed to be less than the original, while the copy (?) of Korby had rather crude-looking mechanical parts inside.
Timo Saloniemi