I had a program in a subfolder on my desktop, and I had set it as the default program for opening .PK3 and .WAD files, and then, like a total idiot, I moved the program to a different folder.
The next time I tried to open a PK3, the "open with..." dialog box came up. I browsed for the new location of the program, and clicked ok.
But for some reason the program hadn't shown up on the list, so i had unwittingly set it to open with Adobe Reader (the first on the list).
i tried going into HKEY_CLASSES_ROOT in the registry editor, deleting .pk3, .wad, pk3_auto_file and wad_auto_file, and restarting my pc, but nothing changed.