The HB presents are designed for optimal settings for the device you will view them on. However it should not prevent the movie from not playing at all.
Are you adding the movies to the device (iPad) or trying to share via itunes/homesharing?
Sorry for delayed response. I've tried to view our Blu Ray rips on my iPad 2 through home sharing. These ATV3 HB encodes do not even show up as options in our shared library within the iPad 2-- only the DVD rips.
On a side note, I have an iPhone 5, and the files show up in the shared library and play fine on it.
if they are 1080p files with a high bitrate or are files without an AC3 track they will not play on older iDevices. If you are using the ATV3 HB setting you should have 2 audio tracks, so I'm assuming it would be the high bitrate.
You will be able to play any of your files if you either use the ATV2 preset, or if you lower the bitrate of your files. You can do this either by adjusting the CQ slider if you use that, or by lowering the bitrate amount if you do Variable Bit Rate encodes.
I've found that I can't play 1080p files at all even from iTunes over homesharing on either my 4S or iPad 1. Not sure what the problem is, but either way it isn't anything to do with what you are doing currently, maybe an iOS problem? An expert would probably give you a definitive answer.