How do I make Acrobat show only the window on the taskbar?

Not that I know of. Though I'm curious why you'd want it to be that way.

When you have two files open, you have two tabs in the application window and two "open windows" for open files shown when you hover over the Acrobat icon ... because you have two files open. When you go to the Acrobat applications window, only one document should be showing unless you dragged out one of the tabs to create a second window, or you used one of the View>Tile menu command options to separate the combined application window into two of them. And in that case, all you'd need to do is drag and drop the tab from one window back into the other to create a one-piece, two-tab application window once again.

I guess what I'm really saying is from what I'm inferring you're describing a handy and useful feature, and not a bug. If I've got it wrong, please let me know where and I'm happy to do my best to help you. 

Hope this helps,

Randy