To pickup on this old thread, since I was just wondering the same thing:
Using 0.3.1, I have configured Roundcube to not hide messages marked as deleted. If I move a message from the inbox somewhere else (like the Trash folder), it gets moved, not just copied and marked as deleted in the inbox.
I guess, there is just no point in having that option with that configuration, right?
Also, I think "Compact" (or "Packen" in German) is not the right word for this operation (since it sounds more like something is going to be archived or compressed), if actually it is supposed to purge messages marked as deleted, which can end badly, like in ivan8r's case.