I've been unable to find a common factor other than "projects I've used Merge to bring modules into", so I'm posting here to see if anyone else has run into the same issue:
Frequently, in projects I've added modules to via Merge, some workflow functions stop working or work infrequently. Symptoms are usually being unable to double-click generator names on the Playlist to bring them to the forefront, and some context menus (like the Stream Options window that appears when using File->Stream To File...) won't appear until I press Alt.