I found this the case as well, but sometimes it's how bass-ackwards the installer was.
In the case of my mom's boyfriend's system, he decided to get all backwards, and made it so you need THREE REMOTES to change sources. Bad part is my mom is not very technology inclined (she jsut wants things to work and be intuitive), and he likes to play with anything electronic in a 50000000ft radius, and usually ends with my cursing him out when he's in my apartment for messing up my receiver settings again.
Needless to say I bought my mom a single learning remote and programmed it for her, then opened it up and removed the segment of circuitboard that the program button resided on, so he can't even attempt to re-program it (he has a bad habit of this, I had to pimpsmack him for trying to mess with the delay settings on my receiver last time he was over).
Needless to say, her remote works far better....now the only problem is he keeps walking off with it and losing it in the house....so next time I visit, I'm installing a remote finder on it.