You must use SqueakConsole.exe; Windows is badly broken like that. Command line arguments are not passed along for Squeak.exe.
When the system is running you can check that the arguments are available via getSystemAttribute: and senders (eg Squeak has SmalltalkImage>>rawArguments and SmalltalkImage>>arguments; not sure what Cuis provides).
So, I checked the available system attributes w/ `getSystemAttribute:` in Cuis and saw that all my Windows command line args are passed into the image as system attributes properly on SqueakConsole.exe _and_ Squeak.exe. After I did a few changes to my Cuis image, I was able to get my start-up script running! I'm confident the issue here is actually related to the Cuis image and has nothing to do with OpenSmalltalk. I'll go ahead and close this issue and let the Cuis maintainers know.
Thanks for the help!