No problems here either, don't know why you would have gotten a program update automatically if you had that set to ask.
The default settings, auto for defs and ask for program updates, are probably the most practical since the latter are much bigger and frequently require a reboot and you'll probably want to hold off till a more convenient time. If I get that popup notification of a program, I'll make a mental note to check for updates later -- or, of course, there's that view-latest-popup feature, assuming there hasn't also been a defs update in the meantime. That "update now" link still works if you're viewing last popup, by the way.