I've always specified the full file path when using open, I don't know what happens if you do something like open("Blah", 0);
Anyway, the only cause where that will happen is if you specify the file name with md0=filename (actually it'll probably look in at bt(0,0)/filename (or /filename) if you don't specify the full path).
Basically, it'll check the user specified filename, where ever it might be, then it'll check in /Extra, lastly, it'll fallback to a patch I use in NBI (Postboot.img).