Hello. Thank you for contacting the Toolset support.
- The wpml folder in uploads: yes, that one is from us.
It is created by the OTGS Installer, the shared component that handles licensing and updates and ships inside every OnTheGoSystems plugin (Types,Views, Forms, and WPML alike).
In a recent installer version, which Types 3.6.3 bundles, we moved the per-plugin update changelogs out of the database and into a single compressed file at:
wp-content/uploads/wpml/changelog.txt.
That is the new directory you are seeing. The reason it is called wpml rather than toolset is purely historical: the installer originated with WPML and uses that one shared namespace across all our products, so you get the same folder name even on a Toolset-only site. It is harmless, and it is actually a small improvement: that changelog data used to sit in an autoloaded option in wp_options, and moving it to a file keeps your options table leaner. You can safely leave it in place.
The mnx_versions option: that one is not ours. I checked our entire codebase, Types, Toolset Common, the OTGS Installer and WPML, and there is no option by that name, and the mnx prefix is not one we use (ours are otgs_, wpml_, icl_, wpv_, types_ and similar). An option that records a snapshot of your installed plugins and themes is the signature of a site-management, monitoring, backup, or security tool, or a hosting control-panel agent. Those tools watch for plugin and theme changes, so updating any plugin, Types included, is exactly the kind of event that makes one of them re-scan and write its inventory. That timing is almost certainly why it showed up right after the Types update, but the writer is a different plugin or service, not Types.
If you would like to pin down which one, the quickest way is to search your site files for the string. Over SSH or in a file manager, from wp-content, run grep -rl "__mnx_versions" plugins/mu-plugins, and whichever plugin contains it is the one creating the option.
If nothing turns up there, it is likely a host-level or external management agent rather than a WordPress plugin.