After debugging it for a while, I found the problem to be that URLScan had been installed on the server (Windows 2000 Server), which was preventing any requests with dots in the folder name.
URL Scan is a tool that MS suggested everyone install a while back that acts to filter out many malicious attacks.
So, with the default settings any request for a file inside the scriptsSystem.Web.Extensions folder would be denied as a 404 b/c of URL Scan.
To fix this, you need to edit the UrlScan.ini file, located in %WINDIR%System32InetsrvURLscan. Near the top of the file, change AllowDotInPath from 0 to 1.
The run iisreset to restart IIS and you should be ok!
More info on URLScan is available here: