The mouse transparency does not work correctly in arcanum, it often shows a black box around it, or random mess, or a picture of what was under it when the game first loaded. 2d mode natually fix it, but 2d mode gets low single digit FPS. Is there a way to fix the mouse and only the mouse? maybe set software mode for mouse only while 3d mode for everything else?
I also had a black box around my cursor at first, but the -doublebuffer commandline parameter seems to work for me. I don't use -no3d. Remember to turn on XP SP2 compatibility mode, and disable visual themes and desktop composition.
Are you running XP or Vista? If you go into "Control Panel" and select "mouse options" the mouse transparency should be in there. If not, disable Vista's transparency (ie: put it in display compatibility mode)