Did some file comparison after moving the Preferences Windows around and looks like it's stored in the C:\Users\(username)\AppData\Roaming\WACUP\winamp.ini file in the [Winamp] section with the following lines:
pref_wh=119 (default seem to be 0, this is after I lengthened it.. can't change the width of the Window)
pref_wx=789
pref_wy=100