I had this exact same problem. After hours of frustrating attempts to find out what was causing this, I stumbled across a fix.
It seems that Eclipse can't write to files with the 'hidden' attribute set. For some reason my .classpath and .project files had the "hidden" attribute set.
(No doubt some helpful process or other thought that because they started with '.', they should be hidden)
Unsetting the "hidden" attribute fixed the problem. ("attrib /s -h" in your workspace directory for those who like the command line)