i've never had a problem with the light linker node, but sometimes, if you parent your persp camera to a node (which some artists sometimes do around here), and then reference that scene, then you get two persp cameras in the scene.
but maya doesn't count the referenced persp camera as a referenced camera, and imports it as an actual camera. so to unreferecne that scene, you have to unparent the persp cam, and then un-reference the scene.
of course, guess what sometimes happens when you try to delete that non-referenced referenced persp camera? you guessed it, it says, read-only node, can't delete.
of course, this doesn't happen ALL the time, only sometimes.
but, no, i don't have an answer to your question. just thought i'd jump on the "venting" bandwagon. 