Further research resulted in a better solution than I reported before.

Launch the installer from a command prompt, using syntax like:  KG411Setup.exe -r: c:\temp\silent.ini

This will launch the installation wizard.  Click through it, selecting the options you normally would. On the last page, uncheck the boxes for display PDF and read me documentation.

You should now find a silent.ini file in C:\temp (or any other path you specified in the above command line).

To run the install silently, use:  KG411Setup.exe -p: c:\temp\silent.ini

At the end of the install, it will still open an Explorer window on the Start Menu shortcuts for KaleidaGraph. I could not find a way around that... but this should help a lot on silent installation.

If the version 4.1 installer is called with the "/s" switch, it will install silently.  Unfortunately, it will also pop up a Windows Explorer window on the shortcuts in the Start Menu, open a PDF file, and open a readme file.

I got rid of the opening of the PDF file and readme file by adding code to my deployment script which killed any "rundll32.exe" process object which had a CommandLine property containing "KaleidaGraph" in it.  I couldn't get rid of the opening of the shortcut menu.  I'll post the script code in the Script section in case you find it of value.

For uninstall, you call "C:\windows\unvise32.exe" with the "/s" switch and the path to the "uninstal.log" file inside the KaleidaGraph install directory.  For example:

C:\Windows\unvise32.exe /s C:\Program Files (x86)\KaleidaGraph 4.1\uninstal.log

(They don't seem to want quotes around the path, BTW.)

Here is the script I used to kill the PDF and readme opening prompts after silent installation of KaleidaGraph.  (It's taken from my standard deployment script and may reference objects which aren't created here, so some tinkering may be necessary.)

   Dim dllProcs, thisProc 
   For i = 0 To 60
       WScript.Sleep 1000
       dllProcs = GetMatchingProcessObjs("rundll32.exe")
       
       If IsNull(dllProcs) Then
          Exit For
       End if
       
       For Each thisProc In dllProcs
       
          If InStr(1,thisProc.CommandLine,"KaleidaGraph")>0 Then
             thisProc.terminate
          End If
       
       next
   
   next


    Public Function GetMatchingProcessObjs(processName)
          
       Dim objWMIService, procsFound, matchingProcs(), thisProc
       ReDim matchingProcs(0)
       
       Set objWMIService = GetObject("winmgmts:\\.\root\CIMV2") 
       Set procsFound = objWMIService.ExecQuery( _
            "SELECT * FROM Win32_Process WHERE Name='" & processName & "'",,48) 
       
          
       ' Restructure the collection as an array, to make it easier to
       ' specify a process by index.   
       For Each thisProc In procsFound  
          
          If IsNull(matchingProcs(0)) Or IsEmpty(matchingProcs(0)) Then
             Set matchingProcs(0) = thisProc
          Else
             ReDim Preserve matchingProcs(UBound(matchingProcs)+1)
             Set matchingProcs(UBound(matchingProcs)) = thisProc
          End if
          
       Next
               
       If isnull(matchingProcs) Or IsEmpty(matchingProcs) Then
          GetMatchingProcessObjs = Null
       Else
          GetMatchingProcessObjs = matchingProcs
       End If
       
    End Function

This application doesn't run smoothly on Windows 7 64-bit.  This is because it writes to a KGOleSrv.INI file in the Windows directory and to various settings files inside the Program Files directory.  The application also wants to write to protected areas of the registry at each launch.

To resolve those issues, I installed to a different location (e.g., C:\Products) and made that writable to non-administrator users.  Then, I included the INI File from the Windows directory in my deployment script.  This was copied to the Windows directory and permissions granted so that users could write to it.

The final issue, the registry problem, required creating a Compatibility Shim that runs the application in Windows XP SP2 compatibility mode.

Serialization information for this software gets stored in HKLM\Software\Synergy in a key with a random-looking name and value, and in the files KG41License and KGraph.rsr inside the installation directory.  If you register the product and capture that information, you can deploy the product in a registered form by applying those items after installing KaleidaGraph.