it a very odd problem however i've found it actually on occurs with people who haven't actually purchased a registration

you require a file called ms3d9x.reg or ms3dxp.reg unless you have that within the milkshape directory when it registers it all it actually achieves is logging your serial number, as each reg file is compiled specifically to a single serial code you can't simply copy one from a working copy

i'd suggest you contact mete at
chumba@hispeed.ch as thats the official support email...
also i wouldn't try opening up one of the .reg files

they've been designed to become COMPLETELY useless if tampered with.
Anata aru kowagaru no watashi! 