Hi @thomasn, Software Updater is surely doing something unusual. Like you said, it's probably so it doesn't interfere. But this behavior is also causing strangeness in compiz:
It's well down the topic before I found out it was compiz-only.
Sorry no solution but I have to think these are somehow related as they both occur with the minimized appearance of an update from Software Manager. I don't use a dock but I'm curious if you also happen to be running compiz as your window manager?