The command prompt full of text is probably mame.cmd when it errors out. You can trying inserting a line in mame.cmd with the word "pause" in various places so that you can determine which line is causing the error. You may need to tell Mala to use a normal window for Mame instead of a hidden window to properly see the error after you insert some pauses. If you get the window to pause, hopefully you can see exactly what the error is.
You can post your mame.cmd and the pertinent entries of your mame.xml or combined.xml (whichever you use) along with a screenshot of your mame settings if you want to.
In Mala, is your mame command line %rom% %path%? Notice the space between the two entries. Also you mentioned that the games show up in the list. Do they show up after right-clicking and choosing "refresh main game list"? If they no longer show up, the entries in your xml file may not be there any longer. If you created a combined.xml file which has your new entries, is Mala still pointing to that xml file?
Just a lot of shots in the dark...