Gerben,
Before I start setting up a new context, say domain1, I run a simple test: I create an index.html file in the domain's home directory, ie.., teg ine where the domain's index.php file is) that just contains something like "Welcome to domain1!".
If I can see its contents by entering in the browser the file's URL (in this case,
https://www.domain1.nl/index.html), I can be sure the virtual host has been configured correctly. This tells me than that any issue has to be caused by that context's settings.
Also, say I am working in my MODX manager at
https://www.modxserver.nl/web/manager on a page called domain1page.html in the domain1 context (I am assuming I have friendly URLs enabled here) as soon as I click the View button to check that page's rendering, the URL in the browser's address bar changes to domain1's URL, i.e,
https://www.domain1.nl/domainpage.html.
Can you run both the above checks on your installation and let us know how they work for you?
Thanks,
Massimo