When ever I do scripting through Test Director. I load the WinRunner with Startup it should show for 10 seconds for selecting the Add-Ins. After doing the scripting I will save the script to the Test Director.
When ever i run the Script with Test Director, if loads with the Add-Ins default, with out any changes.
You can try one thing, just open the WinRunner from your system with Web & Java Add-Ins loaded and close the WinRunner. Then try running the script through TD. I guess it should solve that problem.