When I set up a program, my mind first goes to the database to search the desired sets which then appear in the "selected programs" window of the channel. But, when I then click on "Program Preset" those chosen sets disappear and I must start over again!

As it stands today:

Spooky2 (August and later edition) is designed and written around a left to right sequence. Meaning that presets should come before programs and then settings.
Presets are really just about pre-selecting waveforms & settings and programs - if a preset has zero programs then that is what why it will clear out the ones you have already selected.
If you do skip the preset page, and only do programs page, then all it means is that the generator settings page (waveforms being used etc) are going to be on thier last loaded values.

Working out how to provide this way of working; whilst not confusing people who do it the other way would need to be considered carefully.

For example; if I had just stopped a channel running a healing detox program; and then I then went back to the preset tab and hit a killing preset; I would not want in this case for the detox program to be loaded.
Anyway... that is the developers problem to sort through.

For more details, please check the link:
http://www.spooky2.com/forums/viewtopic.php?f=5&t=6002