I've been using references a lot to get Intellisense to "know" about all my scripts that have important variables and functions. To make this easy, I've been including a single reference on all of my scripts:
/// <reference file="./../references.js" />
references.js is a script that is never run. All it does is contain all my other references I want to use so that they will be populated into Intellisense. With 9 references included in my references.js, everything works fine. But once I add a tenth, things start to bug out; One of those references will no longer be processed into Intellisense, and if I try to edit the script that's not being processed (and try to use Intellisense on it), it waits a bit and then crashes WebMatrix.
I don't know much about debugging this type of thing, but my only idea about what it might be is it could be recursively including those references and hitting some max references limit.
(Apologies if this isn't the correct place to report bugs)