If I recall, The Hellforge Cannon from Demon Eclipse has this same problem. Here's the wad I found this with (it's a work in progress, I'm using a few things from a Q2 expansion pack for it

I tested this in GZDoom 1.0.30 and Skulltag 97d beta 4.3, I can't find the page with the latest ZDoom revision to test this in.
Edit: Oh, I forgot to mention. Hit 'give antimatterbombpickup' in the console, then use it like any other stored inventory item. I fixed up the A_Explode so it's not supposed to hurt the shooter, too, so that's one more indication that it isn't working.