I updated glyphs 2.5b (1094) and installed modules form the add-ons install panel.
Then, I run “Copy Layer to Layer.py” of Glyphs-Scripts/Masters.
The setting window of “Copy Layer to Layer.py” appears and “Note: ‘Copy Layer to Layer’ could not load preferences. Will resort to defaults.” is printed on the Macro panel.
The cursor becomes the rainbow progress, and then it never comes back again…
I restarted Glyphs.app and tried again, it was the exact same satiation.
Is that reproduced on your machine?