In CS 2008 we have our javascript files linked through the scriptresource.axd handler. This is very similar to the webresource.axd handler in that it serves content from within a dll. The gotcha is that the scriptresource handler will throw an exception if the timestamp of the assembly is newer than the current server time... This is not timezone aware.
The result... Your in central time, you compile CS, and deploy it to your server in say pacific time, and vola... you get javascript errors.... why? well the scriptresource.axd will throw an exception because it thinks the dll is invalid because its timestamp is newer than the server time.... the error magically goes away in two hours, because now the server thinks the dll time is ok...
Its important to note, this is not a CS bug, but rather how the Microsoft script handler scriptresource.axd is coded.
To work around the issue, set the time on your development workstation to the same time as your server, before you build.
Dan