We have seen this in earlier versions but I have not seen it in V9.3.1. Please try the following steps and let me know if it works. If it doesn't fix it I will look into it further.
Close out of PADS, open the powerpcb.ini file and search for something like "Options - Size=419 481". The number values will probably be
different so just search for the "Options - Size" portion. Once the line is found delete it from the powerpcb.ini file and restart PADS.
There may be another cause of the cut-off Options box. Please go to Start, Control Panel, Display. In Windows 7 check to see what the setting is on the "Make it easier to read what's on your screen" page. If it is set to anything other than 100% try setting it back to 100% and restart Layout.