There are several reasons why HD reliability suffers in comparison with FM analog:
1) The "importer" (which encodes HD-2 and -3 channels) runs on a Windows platform.
2) A couple of years ago, iBiquity realized that installation of a Windows PC at a transmitter site (subject to lightning, RF, power glitches, temperature variations, etc) isn't a very good idea, and now recommends that the Importer be located at the studio, which is usually a more suitable environment for sensitive electronics.
3) However, this configuration requires an Ethernet connection from studio to transmitter, which in many cases is less reliable than a good-old-fashioned 950 MHz analog STL. Some stations have attempted to use unlicensed spectrum (for example, 915 MHz LanLink) with disappointing results. This paper discusses the challenges of transporting data from studio to transmitter. It costs a lot of money to do it right, so most owners don't:
http://www.bdcast.com/fgal/white_paper/Network_and_STL_for_HD_BCEWHP.pdf
4) Large radio groups have cut back on engineering staff under the false assumption that their expensive new digital equipment is so wondrously reliable that it doesn't require maintenance. Gullible executives at these companies seem to think that the mere act of spending millions of CapEx dollars on HD Radio gear will somehow "position them for the future", without understanding that stations still require qualified
people.
5) Many stations have only one HD-capable transmitter. When it fails, the analog can be restored (thanks to that 25-year-old FM backup rig) but HD is down until repairs to the main system can be made.
6) Some stations must use an auxiliary antenna to transmit the HD signal. During tower maintenance, or in case of failure of the main antenna, the analog transmitter must be patched into the aux antenna, so it's goodbye HD. Who's listening to that, anyway?