Eclipse: Class file name must end with .class

Problem:
Today after I switched to another workspace to work on another CVS branch. I got error in Java search "Class file name must end with .class" when I type Ctrl+Shift+G (for reference in workspace).

Options I tried:

1. Clean all projects and rebuild workspace (not work)
2. Close the projects and reopen again (not work)
3. Close Eclipse and start again (not work)
4. Add -clean in Eclipse startup script (e.g. C:\Workshop\eclipse\eclipse.exe  -clean), and this worked!!

Another option I didn't try:
     a.  Close Eclipse
     b.  Delete <workspace>/.metadata/.plugins/org.eclipse.jdt.core/*.index
     c.  Delete <workspace>/.metadata/.plugins/org.eclipse.jdt.core/savedIndexNames.txt
     d.  Start Eclipse again 

See http://stackoverflow.com/questions/6816/eclipse-class-file-name-must-end-with-class-exception-in-java-search

Root Cause:
Unknown, but mostly like it is Eclipse cache issue. My Eclipse version is as below

Eclipse Platform
Version: 3.4.1
Build id: M20080911-1700