Firstly you could try changing your screen resolution to 1152 x 864. This size handles most machines.
If you're using MFME1 you can press F9 to hide/unhide the menu bar at the top. This gives an extra bit of space for the machine to appear in.
If you're using BFMulator you can scroll the machine up/down by using the wheel on your mouse or the pageup/page down keys. Also ESC hides/unhides the menu bar.
Not sure about JPM as my windows platform doesn't support it, but someone should be able to help you.