I've been a Dish Network Technician for some time now, and due to the increasing number of HD conversions and the low prices of HD televisions out there I have seen numerous HD related issues.
I will tell you that when you call Dish Network and prompt technical support through the menu you get nothing more than an $8 an hour Customer Service Rep sitting at a desk somewhere reading from a computer screen. Their only objective is to get you off the phone as quickly as possible. I wouldn't take anything they've said seriously if I had to. I as a technician always advise people to request to be transferred to an advanced technician for problematic issues. You can easily tell the difference between a tech and a csr through Disn Network because a tech will have a 4 digit id number (ie: "Hi my name is Brian, my tech id is 0000) a csr will have a 3 digit operator id number that always involves letters.
But in my experience as a tech, granted Dish Networks boxes are all mass produced in foregin countries so I definately wouldn't rule out bad HDMI ports on a few. But we're talking of less than a percent of a percent. There are no "software" issues involving the HDMI output of the boxes, it is simply an output it is hardwired to work and is not software driven. The only software on the boxes is used to decode the programming signal and to operate the system menu/program guide. As stated before the HDMI port is simply an output to the television just like the component/composite/rf, there is no software... It simply works, or it doesn't.
A vast majority of the issues lies either within your television set or your home electrical system. Some of the HD televisions (especially Samsungs in my experience) seem to want to backfeed power through the HDMI port into the settop box. In doing this it causes the reciever to have intermittent moments of stupidity and do such things as flash colored screens, disable audio, and even lose signal acquisition all together. The new Dish Network recievers (both the VIP and the K line. ie. VIP211, 222, 612, 622, 722, 211K, 222K, and 722K) work off of a constant current not a variable one like recievers of old used to, so any alteration in current within the reciever itself be it from the wall outlet or television itself can cause unexpected results from your reciever. This is not a stand alone problem with Dish Network recievers either, Time Warner and DirecTV customers are also experiencing similar issues.
After many service calls, reinstalling complete systems, and replacing recievers I have found that most often in cases such as these the TV's are the culprit.
A few tips to find out what the problem is:
1: Check the satellite junction (a silver block in which the cables from the dish meet the cables to the recievers) and ensure it is grounded to a NEC approved grounding location.
2: Verify through the Dish Network reciever via "Menu 6-1-1" (ie: the "Point Dish Screen) that your signal strength on all satellites is abouve the "minimum" (often 65 or greater) with the exception of the Eastern Arc 1000.4 (61.5, 72.7, 77 orbital locations) setup in which 50+ is ok.
3: Through the STB Health Life screen via "Menu 6-1-3 and under details" after test is complete ensure Values 0-9 report no abnormal numbers (-1, -2, 0, 2, 4, 200) are normal, something like 33 or 109 would be considered abnormal and depending on which value (0-9) is being reported could indicate reciever malfunction. If so call Dish Network (with Value info) an RA the reciever.
4: Lastly, if all above checks out ok. Disconnect the HDMI cable from the reciever and "drag" the metal end of the cable flat against the metal housing on the back of the reciever while the Tv is active on that input (ie: HDMI1, HDMI2 or w/e) and look for ANY form of static discharge or arcing between the two pieces of metal. (minimal to no lighting works best as this will not be a substansial arc, but will definately be visable). If this is the case, your television is "backfeeding" power into your satellite system, and is the resoning for your troubles. Switch to a component input and your problem will be resolved, then call your Tv manufacturer to have the issue corrected.
Hope I've helped.