I have an HDHomeRun (HDHR t1 us), and this device only has one usable tuner, though LinuxMCE detects 2. I presume the second is some sort of fake to allow recording one thing and watching another. I have a couple of crap cards that do the same thing, though I know there is only one usable tuner. Snapshot 22982 (or later) with the MythTV .23 shoehorn prioritizes the fake tuner and will not access the correct one before crashing. Deleting the tuners and redefining the single usable tuner gets overwritten as soon as the changes are applied (presumably after mythfilldatabase is run).
In order to prevent this, or more accurately allow your changes in MythTV Setup to be applied and not overwritten, in the web admin drop to device tree/Core/DCERouter/Myth TV Plugin. Towards the bottom of the page is a checkbox which says "Dont autoconfigure"
Then delete all, define card/input, and when it says mythtv is ready... it is. I am sure many of you are already aware of that checkbox... but it cost me almost 2 days... so naturally I think it's discovery is like finding Atlantis. Hope this helps someone having troubles.
I use an HDHR DVB-T version here in the UK and apart from different firmware the hardware is the same. Unless I am misunderstanding you (if i am sorry!) you are not saying that your 2nd Tuner has a hardware fault. This would imply that the PnP script for the HDHR is not quite configuring it correctly...so you should report that if thats the case. Alternatively what you could do is manually setup the 2nd tuner using mythtv-setup at the Core. It sounds like you 2nd tuner has not had a source mapped to it correctly as both tuners should be usable in an HDHR...if your not using multi-rec then having two tuners allows you to record/watch two TV channels simultaneously. If you are using multi-rec then you can record/watch up to 5 channels on each Tuner (these settings can be configured in mythtv-setup)
All the best