Can you try generating the WebHelp to some other location. Also if you are using Win7 OS then please make sure that you have proper read/write access to the folder in which you are generating WebHelp.
Here is a long shot, but a similar issue plagued all our writers: Is your RoboHelp installed silently? We have found that the whxdata files were not created correctly when RoboHelp was installed silently.
Our solution was to uninstal Robo, manually install the trial and call IT to enter the license key.