Windows 7: Help with not minimizing windows to System Tray

I have a problem that's backwards to most questions that I've seen. I have two windows, say Window A and B. Buttons for both show on my taskbar. In the past, I've been able to toggle between the two by clicking on the taskbar button for the window that is on top.

So, if window A is on top, I could click on its taskbar button and that would minimize window A to the taskbar, showing window b. When I wanted to see window A, again, I could click on its taskbar button, and it would again display window A on top of window b.

Now, when I click the taskbar button for window a, the window minimizes to the System Tray, instead of the taskbar. The toggle function that I found so handy is broken.

There must be some setting that's gotten flipped, but I can't find it, and every question that I look at is from someone who wants to have windows minimized to the taskbar.

Thanks for your help!

What are the applications in question? Because its not a function or setting of Windows itself but one of the application.

I'll check, when I get home.