It seems odd to be typing the Go command into the command field manually. Am I missing something?
(You can type the argument you want directly, e.g. OPENINDUAL, but I can't think of a situation where it makes sense to do that either, when you can switch to the other side and type C:\Windows on its own.)
Using a Go C:\Windows USEQUALKEYS test command in a CLI window...
Enter opens C:\Windows in the current tab (as expected)
Shift-Enter opens C:\Windows in a new lister (as expected)
Ctrl-Enter does nothing (expected it would open C:\Windows in dual)
Alt-Enter generates an error sound and does nothing (expected it would open C:\Windows in a new tab)
Alt-Enter works for me (CTRL does not of course). It seems there is something to tweak in your configuration, so at least one more qualifier can be used on your system in combination with your usercommands.