2016-09-01, MDP2 (v. 2.3)
This bug has been fixed in MD 1.6.3. If you are still having issues, it might be due to a bug: Presets for Groups are not saved properly if subcontrols are set to "Reset to Defaults -> Exclude"... shut this toggle off (NOT blue).
We've reconfirmed this bug in 1.6.2+, but now there's an easy workaround.
The presets used in Preset Groups and Channel Changers save normally. However, when a .mididesigner file is mailed or saved and loaded (not automatically), the presets are missing.
Ensure that you have at least one global preset in your layout (on iPad, use "Save" from the "More" menu).