I had the same issue, I did the following to fix the problem.
gen - automated code in project (from dependencies and references)
src - source code in project
There was no need to restart the Eclipse. It just started working.
Honestly I have never tried "Android Tools > Fix Project Properties", sometimes it might be doing the same thing. I do not know, I just did above after seen the error message, thinking something is wrong with the build paths.
Edit
Later on it was not sufficient, I was getting the error again. Then I "checked" all the dependencies listed in that view. Now it works again. So far so good. I will keep this updated if it fails again.
FYI: in my last attempt, I tried "Android Tools > Fix Project Properties", but it didn't work out for me.