I've seen this too. Some programs go into hiding when they are minimized and cannot be invoked with Alt-Tab anymore (LeechFTP for example, if I remember correctly). The point howver is that all of these programs I've seen do put their icon into the systray for easy access, nullifying the possible harm caused.

And... when you know that the LS systray just fails to show some things it should (the Windows update -screen for example) and add 1 + 1... well, it was to be expected that something like this happens.

Usually, when faced by problems like that, I look into finding a less buggy program, it seems that there's nothing you can do.