I had this problem. After some troubleshooting (bypassing of the switch, trading out LNB's, and checing connections (similar to what's mentioned above)), I isolated it down to an LNB that was malfunctioning sporadically (but more and more frequently). I purchased a new one on ebay, swapped it out, and have had no problems since.
This COULD be what's wrong with yours... but understand it might be something else. If you're a tech geek like me (or know somebody who is), you could try to isolate the problem. Your other option, of course, is to have DN come out and look & replace the culprit.
Just because it says there's a problem with the switch, doesn't always necessarily mean that it is a problem with the switch. A bad LNB can 'confuse' the switch and ultimately 'confuse' the receiver....