It is obvious that since the main computer had over a thousand unaccounted runners, and believed there to be a Sanctuary, it was unaware that Box was collecting them for protien.

Did Box Pre-date the computer system, or did he have a short in his circuits which caused him to collect the runners for protien, without the computers knowledge.

Is this explained in the book.

In Goodman's Screenplay Box runs the freezer system where food from the marine breeding complex was stored. The system was abandoned,but Box went on passing the time with his ice sculpture and freezing anyone who showed up,like Runners,as he once froze fish and plankton.
This information is almost totally lost in the film due to the editing job that was done,especially the deleted scene.
The novel is no help since it's handling of Box was completely different.
So,I believe Box pre-dated the computer system.