Okay, this now works for FS command and for JS:

Code:
<SCRIPT LANGUAGE="JavaScript"> 
<!--
function DoAlert()
{ 
 document.write('got here<br>');
 alert("HERE");
}

function seq_DoFSCommand(command, args)
{ 
 alert("FS got through");
}
//--> 
</SCRIPT> 

<SCRIPT LANGUAGE="VBScript">
<!-- 
//  Handle IE.
Sub seq_FSCommand(ByVal command, ByVal args)
    call seq_DoFSCommand(command, args)
end sub
//-->
</SCRIPT>

                    </HEAD><BODY BGCOLOR="#FFFFFF">

<OBJECT	CLASSID="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
 WIDTH="100%"
 HEIGHT="100%"
 CODEBASE="http://active.macromedia.com/flash3/cabs/"
 ID=seq>
 <PARAM NAME="MOVIE" VALUE="seq.swf">
 <PARAM NAME="PLAY" VALUE="true">
 <PARAM NAME="LOOP" VALUE="true">	
 <PARAM NAME="QUALITY" VALUE="high">
 <PARAM NAME="SCALE" VALUE="SHOWALL">

 <EMBED
  NAME="seq"
  SRC="seq.swf"
  WIDTH="100%"
  HEIGHT="100%"
  PLAY="true" 
  LOOP="true"
  QUALITY="high"
  SCALE="SHOWALL" 
  swLiveConnect="true"
  PLUGINSPAGE="http://www.macromedia.com/shockwave/download/"
 </EMBED>
</OBJECT>
In this instance the fsCommand used can be anything, with no args, as the above does not check for anything. :)

Syntax of the JS is:
Code:
Javascript:DoAlert();void(0);
and the void eliminates the new window prob. Thanks.

Reason JS was not handling it before appears to be (this is too silly) case sensitivity (lowercase D in DoAlert in the KoolMoves dialogue box - my bad. *dons dunces cap*)

Thanks again.

Now to see if I can pass info the other way, without stupid mistakes. lol.

Hmmm. I wonder if it is possible to create forms / text fields in KoolMoves.