Thanks for your support for AgUnit !
About the debugging issue, it certainly is not expected to break the regular debugging. I use this daily without any problems.
What you should check first is to make sure the "Silverlight" checkbox on the "Web" tab of the properties of your web project is checked.
Without that, Silverlight debugging won't work when you debug the web project.
You should also avoid debugging with any other browser than internet explorer, I've experienced issues with debugging in both firefox and chrome.
This is usually due to your browser caching the .xap file. Try clearing your browser cache to see if that helps, maybe even try in another browser ...
If none of that works, can you try creating a new web and silverlight project and see if that works ?
AgUnit should not interfere with runtime debugging, it's a purely a plugin for the resharper unit test runner.
If you can't find the problem, let me know what version of visual studio, resharper, silverlight and the silverlight sdk you are using (you can find them in programs and features in the windows control panel).
This way I can try to reproduce the problem.