I encountered this problem and then stumbled onto a resolution.
At first when I was running the JMeter test plan, I was relying on the View Results Tree to write the csv file output, which in turn was used to generate the graphs. But there were 2 problems: First at test end there were GUI pop-up alerts from JMeter saying "Error loading results file - see log file", and secondly the graph themselves actually contained the text "Waiting for samples...".
Looking at the jmeter log, I found: "jmeter.save.CSVSaveService: /path/to/my/test-results.csv does not appear to have a valid header. Using default configuration"
Then I tried adding the Simple Data Writer. I noticed that the View Results Tree csv file output did not contain any headers, but the Simple Data Writer csv file did have headers. When I changed the graph generator to use that one instead the errors went away and my graphs actually were graphs as expected.