Peter,
Although I'm new to the TVHeadend world (just setup my first one last week), I am using an HDHomeRun Dual (that I had lying around) successfully with both tuners. I know in the beginning I only had one tuner working until I wrapped my head around how it worked and what I was missing.
I'll try to help- but I'm no expert!
Make sure you have the same "Network" selected for the second adapter as you do the first. The setting is found in the "Parameters" box that pops up when you go to Configuration->DVB Inputs->TV Adapters.
Also, make sure that TVHeadend sees both tuners as ATSC- the issue I had when I set mine up was that I accidentally configured one tuner as a DVB-T tuner and had to fix my error in the config file.