you uninstalled the game while you still had some mods installed so it did not uninstall properly and left files behind
when the game uninstalls it leaves ALL modded files there because they arent recognised, this includes the jsgme utility.
uninstall the game then locate your main sh4 folder in whatever directory you installed it to and manually delete it.
now your saved games are most likely all corrupted too by this point so open the documents folder and just delete that folder too.
reinstall the game, then install jsgme, then put your mods in jsgme and activate the ones you want
