It would appear that I did not solve quite all the compatibility issues between Silverstripe and my web-host. Yesterday I was unable to upload files. The problem? It was once-again searching for files in the wrong locations. For some reason, it still insists on prepending "/admin/assets" to URLs - sometimes multiple times - when in the file uploads section.

Whilst this site looked like it was working just fine, I was having some trouble with the CMS. For example, the security, comments and files & images administration pages weren't working. On the public part of the site, the blog tags and archive links resulted in "page not found" errors.