Not had this but my key fob is doing pretty well! Iv dropped it in the bucket of water i was washing my car with and its been stepped on, sat on and dropped out of a second floor window and landed on concrete twice (should have known women cant catch or throw!) and it still works!
What is normally meant to happen is when you put the key in the ignition and turn it, a signal is sent out to check if the keyfob is present. If it doesn't detect the keyfob or it is damaged/battery is flat etc, then the immobiliser will not deactivate.
The problem I was getting was that every time I tried to start the engine, I had to manually deactivate the imobiliser because it wasn't detecting my fob. After taking the fob apart I noticed that one of the contactors connecting to the battery was broken. A quick bit of soldering sorted this problem out and it works fine now.