Where do files go when I upload them via the Update Manager in the web gui????
/var/cache/openmediavault/archives/
There is a file called packages there too. If you have a package (or plugin) that was uninstalled yet seems stuck in the plugin section, or updates section this is where you want to look. You can delete the package out of that archive and be sure to edit the packages file. Make sure you edit out any package you removed from the archives folder.