I believe I understand how permissions cascade in jDownloads and I concur that this is essentially a Joomla! issue.
It is not a timeout: when you change the value of the permission in the select, Joomla! tries to start an AJAX request, but it encounters an error in /media/system/js/permissions.js building the parameters
to be sent to the server.
The error message is
document.getElementById(jform_title) is null.
and a "value" property"). Categories, user groups, etc., all have a field named "title", and everything works.
I'm sorry if I'm not being clear.