I’m a bit late reporting the fix on this one, but TiVo’s new software version (7.2.1) fixes the with the Hughes HTL-HD and similar boxes. The most recent software update adds the old serial control protocol back; see see these instructions for configuration information.
Although I received the new software about a week ago, I was unable to set up serial control until I returned home from a trip and switched out the cables. Thankfully, my Xantech emitter is back in the storage bin where it belongs. It was a great short-term solution, but I’m glad to be back with the more reliable channel changing method.