After doing some pretty extensive testing of the alternate tunings I noticed that there was a fundamental problem in the way we were calculating the tunings while trying to add editing capabilities to the synth. Specifically, the calculation pushes the note into the alternate tuning table after the mods are calculated, resulting in some unexpected behavior. Although this is clearly an error in implementation, we chose not to roll out a complete fix to production to prevent people who have already grown accustomed to the behavior to have an issue restoring their sounds the way they want. However I thought it was a serious enough issue to warrant a fix.
Please note, the OS is not officially supported and I'm fixing bugs on my own time if any arise. It has already been tested but it is possible some problems will come up. Please back up your work before asking for the OS
Edit: Decided it was just easier to post it here... file is attached
Hold down transpose up and transpose down on the keyboard, or glide/portamento on the module, then hit the arp hold button. That gets you into scale edit mode in the FX section of the keyboard. Hit a key to select a note (or the first encoder) and then use the other 3 encoders to alter tunings for that key. Hit arp hold again to exit scale edit mode and save the scale
Also you can export the currently selected scale over MIDI by holding 'Preset' and hitting button 2
Enjoy!