Don't use the 'D' which is for passing Java parameters/arguments.
<gel:script
xmlns:gel="jelly:com.niku.union.gel.GELTagLibrary"
>
<gel:parameter var="from_cmd_line" default="not set" />
<gel:out>Parameter set from cmd line: ${from_cmd_line}</gel:out>
</gel:script>
C:\ProjectX>\Clarity\12.1.3\bin\gel -script cmd_line.gel
Parameter set from cmd line: not set
C:\ProjectX>\Clarity\12.1.3\bin\gel -script cmd_line.gel -from_cmd_line=qwerty
Parameter set from cmd line: qwerty
C:\ProjectX>