Good catch Corion! In my suggestion on the original thread I had escaped the dollar sign so that "$/" would be passed to ss.exe. VSS commands use $/ as the root project path.

 my $cmd = "\"$sspath\\ss.exe\" Checkin \"\$/DMS MW/SCADA/Substation E
+ditor F
+iles/$filename\" -C\"$comment\" -I- -GL\"$checkout_path \"";
[download]

This is likely to solve the user issues in the OP since as you pointed out the newline puts the -Yadmin option on a different command line in the command session.