I recently upgraded from Doxygen 1.8.4 and GraphViz 2.36 where I had no problems generating graphs to Doxygen 1.8.7 and GraphViz 2.38 and cannot now get graphs.
I also encountered this problem. I tried lots of methods mentioned in the net, but failed.
Finally, I have downgraded to GraphViz 2.38 and the problem has disappeared. Now my doxygen version is 1.8 and my graphviz version is 2.38.