Machiel92
appcd 1.6.0 includes a change to the try_files directive which adds the $args variable. I believe this fixes most of the WordPress issues people had. Sites which require more complex rewrites may still be troublesome until we expose more advanced rule sets in the UI.
To trigger a virtualhost rebuild, toggle "force https" or edit one of the rewrites in the panel. This will ensure you have the latest version of the virtualhost config.
If you've got a site which you think should work which doesn't, send in a support ticket and we can take a look.