This is an issue that was introduced in UR1 of Dynamics 2013.
We follow an identical process with our product and we hit this same problem after upgrading.
What is happening is that there is some JS code buried deep inside Microsofts Dyanamics JS, that is called before you navigate to a new area from the site map. This code tries to interrogate the main content iframe - presumably to check for unsaved changes, or generate the crumb trail.
However, where your ASPX page is the content of that IFrame it hits a Cross-Domain "Access Denied" error when trying to access the Iframe, and the rest of their code drops out and leaves you with a blank screen.
The workaround for us was to change our Web Resource that performs the redirect to include a full-size Iframe and set the source of that to our ASPX page - in essence you result in having and iframe within an iframe. So when Dynamics later comes to try and talk to the main Content Iframe, it is still the original web resource, and no longer cross-domain so the JS doesn't break.