When I first put it on, after 15 minutes or so, the source changes automatically. It always goes to the CD source. After I change it back manually, it doesn't happen again. Anyone have any ideas why this happening and what I can do about it? Thanks.
Unfortunately you most likley have trouble in the flip/flop switching circuit. It won't be discrete transistors anymore, but an IC controlling all of that input switching.
Most likely that part of the IC has become unstable. It has a heat range where this is occurring. When cold it is OK, and when it heats up a bit more it is stable. Unfortunately over time this circuit will tend to default to CD all the time.
You might be lucky in that it is a software problem, so try a default back to factory default and do the set up again.
Unfortunately this is not an uncommon fault with these types of circuits, which I have encountered before.
If it needs service in this day and age the boards are rarely serviceable, and so the board with that circuit will need to be replaced if a reset does not do the trick.