When MA3 is in window, and tries to pop up front, it also causes the TASK BAR button to flash, which then causes my auto-hide TASK BAR to un-hide. The task bar then stays up until I click on the MA3 button, letting the task bar hide again. This is a minor problem, since my task bar has a lot of info on it, I like to keep it out of the way. When it pops up, and doesn't go back by itself, I need to find the offending program (many do this by the way) and click its task button to make it happy again, then the task bar will go down again.
Would be great if the aquarium didn't cause that to happen too.
Certainly something that bears fixing.
In the meantime, if (whatever your OS is) can run TWEAKUI, that has the capability to turn off taskbar flashing, as I recall.