"Trained Chipmunk" is a metaphor for those situations where, no matter how automated everything is, you still need to have someone go over to a box and reset/unplug/fiddle with it physically.
Hence the need for a trained chipmunk to do it for us.
Things start to get really wierd when you end up discussing what it would look like on the unit's budget ("trained chipmunks, 1, EUR 200"), what would it cost if it was a certified chipmunk from a big vendor (say, Micronuts or Chipsco), and what would it be like to have to call the support hotline to endure half an hour of Alvin and the Chipmunks music and then hear a reedy helium voice say "Hi, this is Chip, how can I help you?".
Geeks will gladly spend a whole half hour discussing chipmunk scenarios as if they are real engineering problems.
See also the Encarta entry