The one that came with GWX installs directly into the game folder along with GWX, so when you click on the shortcut that was created, it's opening that installation only.
If you downloaded and just did a "default" installation of a newer version and didn't tell it to install itself into your GWX game directory, it probably created a separate installation of JSGME that is not pointed at any game in particular.
I have one installation of JSGME in its own separate folder on my Games HDD, and use different shortcuts that tell it to open in this or that game installation. (See "==1. CENTRAL INSTALLATION==" above.) I completely remove the version of JSGME that "came with" GWX, I don't want separate intallations of JSGME in every game folder that all have to be updated.
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