I haven't had the issue you describe - maybe I'm using it differently?
No, I should've been more accurate in my description. In Rapture, you click on the keytrack window of the Pitch modulator to open up Load Tuning Definition File. You can audition Scala files all day long. But once you use the Shift+click reset to return to standard tuning, the keytrack window "freezes". You can no longer just click on it to change .scl files.
The quick workaround is to close the GUI and re-open it. I also made a standard tuning .scl file in Scala 2.2 to access as a replacement for Shift+click. In DP 1.2, the fix is in, and it's reported to be included in the next update of Rapture.