I haven't saved anything off yet... I probably should do that, now that I am making some patches I actually want to keep. I downloaded a free patch manager thing that was referenced elsewhere on the forum. I should probably set that up today.
Tuning seems completely unrelated to the patches though... It would be rather unfortunate if patches were tuning dependent!
I know what you mean, but if you use certain midi controllers, such as my Oxygen 8 II (now something like 15 years old equipment) and if you try to use a default 0-127 dial to change a square wave on or off on the prophet, then you can end up kind of messing up the settings. I have done that, and I can't tell you exactly what I did. It just messed it up.
However I have had some tuning problems but that was in the distant past. If you don't move it that's probably the best thing. And use it a lot. I had a few days of bizarre sounds in a new location, but then it settled in and I have had no problems with it since.
The patches come up the way they should. The tuning is off if the patches have programmed it off. There are several knobs that are related to tuning in a patch, such as the poly mod and mod frequency options with their governing knobs, oscillator frequencies, Unison detunes, the fine tune, the tuning knob? I don't know I always keep mine in the center and never try saving patches with it off center.
It is easy to save the patches (programs) just download MIDI OX and look in the view tab click Sysex, this opens the sysex view, you go to the sysex tab and click the "sysex dump" and it waits....
now click Global key on prophet, then 6 (top row) global again, then 7 (Bottom row) then use up down keys to left of digits, to choose program, group, bank, user or all. Now the record button sends your program to the computer's waiting MIDI OX program and it displays in the Sysex display window (lower) so you go to save display window in the menus, and choose a name like 558 (description maybe some details?) and it goes to your MIDI OX programs folder. Occasionally I will save a Bank, Group or User. Rarely save any ALL as the factory rarely if ever change. I have thousands of these saved. Ok well hundreds and hundreds at least.