Can you switch to a new workspace and create a new web project, go to the Project properties and see if all the options are visible there. If they are not visible, the installation could be corrupt. In that case I suggest you download our 5.5.1 GA Full Stack installer and setup MyEclipse using that.
If the Project Property options are visible in the new workspace, you should switch back to your old workspace and use the -clean command line argument to clean your original workspace.
http://www.myeclipseide.com/PNphpBB2+file-viewtopic-t-10280.html