Based upon your description, this sounds like it may need servicing, as there's no way to disable ports, and a factory reset would normally be my advice for this kind of issue. The other thing you can do is make sure that you're on the most recent firmware as this may have been a bug that was fixed.
If you decide you want to setup service, here's the thread where you can get details that: http://forums.cnet.com/7723-13973_102-542437/service-issues-click-here-for-help/
Samsung 46d610 HDMI ports not working
Don't know if this issue was addressed on this site - The HDMI ports are not receiving any signal - I have switched out cables, did a restore to factory defaults and unplugged all cables and power cords for 3 hours
I have an old VCR with RCA cables and a DVR with HD Cables.