This is a quick method.
First create a batch file in the mala folder called whatever you want.bat we'll use openmediacenter.bat for this example. If you've never created a batch file before its just a simple text file saved with the .bat extension.
enter this text into the batch file.
C:\Windows\ehome\ehshell.exe /directmedia:general
exit
and save it.
In the mala config in the gui section -> mala exit tab point it to the batch file, you will have to change the selection from just exe to showing all files. This will either start up media center, or in your case it will just maximize it and go to the main panel. You can change the /directmedia:general to other things to have it go to other spots in the media center interface.
I personally haven't done this with mala but I use the C:\Windows\ehome\ehshell.exe /directmedia:general line in a script to run dvdfab automatically and for a few other things and they bring media center right back up so it should work here for you hopefully.
Surprised to see another vista media center user here. We really like ours works much nicer than paying for comcasts dvr and its crappy interface.
Have you checked out emucenter
http://thegreenbutton.com/forums/thread/205829.aspx it works pretty well, it occasionally will forget all your games but if you make the xml file read only then it works really well and it works and looks like a vista media center program. He's getting ready to release a new version soon too.