Seems to me you have 2 sets of issues here: audio and file management. There's no way I can add further to John's info, but I can tell you that he helped me set mine up, and I have my sample buffer set really low as he suggested, with no distortion that you mentioned. I might have mine set at 256 instead of 128, but somewhere in there.
Now, about the save issues:
I don't know if this will help, but I really had a frustrating time learning how to navigate this, and I have figured out how it works for me, without fail.
Let's say I am working on a preset and have changed settings in ALL windows, and want to save them for recall. I go to the mixer page, save the mixer with the name of the kit it goes with. I go to the keymap page, save keymap with the name of the kit. I go to the kit page, and save the kit with its name. THEN, after all of those are all named and saved, I go save the PRESET with the name of the kit (all the names line up, just for my sanity's sake). When I open BFD2 next time, I click "load preset" and choose that preset. Click "load keymap" box at the bottom of the preset load window. This has never failed for me, once I figured out saving all the different windows before saving the preset.
I hope that helps, matey!