Oh ... the following really isn't quite suitable, because in "-basic" mode, I can't change any of the ComEmu settings. I need to still find a different option that tells ConEmu64 not to open up on all virtual desktops.

Based on the comment by @Maximus, I now see that the "-basic" command-line option is what makes the difference and solves my problem:

ConEmu64.exe -basic opens only on the currently active virtual desktop.

ConEmu64.exe [without -basic] opens on all virtual desktops.

The solution ends up being that I just need to use the config file posted above by @JW0914:

https://github.com/JW0914/Wikis/blob/master/Scripts%2BConfigs/ConEmu/ConEmu.xml

Something is amiss about the default config file that gets installed on our Windows hosts at work. Now, all works well with this other config file.

Based on the comment by @Maximus, I now see that the "-basic" command-line option is what makes the difference and solves my problem:

ConEmu64.exe -basic opens only on the currently active virtual desktop.

ConEmu64.exe [without -basic] opens on all virtual desktops.

Oh ... the following really isn't quite suitable, because in "-basic" mode, I can't change any of the ComEmu settings. I need to still find a different option that tells ConEmu64 not to open up on all virtual desktops.

Based on the comment by @Maximus, I now see that the "-basic" command-line option is what makes the difference and solves my problem:

ConEmu64.exe -basic opens only on the currently active virtual desktop.

ConEmu64.exe [without -basic] opens on all virtual desktops.