I'm using AC11, build 1040. I need to download the recent update, which perhaps will solve this. I don't have multiple windows in the walls.
I do, however, have an "existing wall" and "wall to remove" and "new construction wall" co-existing, on dedicated layers with differing layer intersection priorities (it's a remodel project, and I've happily kept layer organization very clean).
I also generate two Elevation views (existing and proposed elevations) from the same Elevation marker, by way of different layer combinations.
Maybe these complexities are confusing the label tool (in it's door/window subset labeling function).
However, Nathan Brauer also is experiencing pesky malfuntions with door/window labelling, and has come up with a cumbersome workaround.
http://archicad-talk.graphisoft.com/viewtopic.php?t=18764&start=0&postdays=0&postorder=asc&highlight...