Uninstalled, but now other plugin settings are lost

After uninstalling Super Cache, most all settings of other plugins are lost. I try to reset them, it says that when I make a change they get saved, but none of them stick. For example, my menu will not display correctly because of this.

What did Super Cache do to cause this problem and how can I fix it?

https://www.ads-software.com/plugins/wp-super-cache/