First, you aren't running the command from Perl. You are opening the file called 'C:\Program Files\Starbase\StarTeam 5.4\stcmd.exe diff'. You need to use a piped open:

open(DODIFF, "$stcmdpath\\stcmd.exe diff |");
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Second, you need to quote the command name for the Windows shell.

open(DODIFF, "\"$stcmdpath\\stcmd.exe\" diff |");
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