This is actually the result of a change from a recent ASP.NET security update. It happens because you have a lot of roles and with the checkboxlists for all the permissions under the permissions tab combinned with all the other form elements it adds up to more than 1000 form elements. The ASP.NET security update set a limit of 1000 and this error happens if there are more than 1000.
I've already fixed this in our source code repository by moving the permissions out of site settings into separate pages to reduce the number of form elements. I will make a new release very soon with this change, but there is an immediate workaround you can use until then. You can put this in user.config
<add key="aspnet:MaxHttpCollectionKeys" value="1500"/>
you may need to experiment with the number depending on how many roles you have, maybe try 2000, and then reduce it as low as possible until the error returns and then put it a little higher so the error does not happen.
You might also review your roles and if you have some that are no longer used remove them.