Ubuntu MATE (Pantheon panel), minimized applications are being closed

I've recently installed Ubuntu Mate 17.04, and I've selected Pantheon as my panel layout.

I've noticed that every time I minimize an application, it's actually closed. (They are even not present in the process list)

Any option I am missing?

Edit: I have to correct myself. I've double checked the processes and they are not dead. It's just that the applications can't be accessed via ALT+Tab, and pressing the icon of the app from the launcher, fires up another instance of it. So it may be an issue with the dock itself.