One notable difference when using R with plots is that the R server needs to create temporary files for the images, which means that the problem could be something to do with R not being able to create files.
You can try running R from the command line on your server, and then running the tempfile() command. If you get an error there, then it will at least point you in the direction of the problem.
What version of WeBWorK and what OS are you using?