I'm adding this as a question/answer so that anyone else frantically trying to figure out what the issues mean know how to resolve it.
The following erratic symptoms appear:
1. Only the Pie Chart gadget does not appear on the dashboards. Instead it displays the error message 'An internal server error occurred when requesting resource.'
2. Some users are unable to attach files to issues
3. Clicking through some links on the 'System' menu shows some errors such as 'Not found (404) /secure/admin/views/configurewhitelist.jsp'. Could not find what you were looking for. Maybe you should raise an issue.