I have been using BEA workshop studio eclipse plugin ( JSP part) with MyEclipse. Bea JSP  workshop( with Struts)  is a very good product – I hope that My Eclipse JSP’s  will be as good the BEA product someday :=).
I had been using MyEclipse (Build id: 20060810-5.0.1-GA windows )with BEA  JSP workshopversion 3.2.1  with no problems. This combination works well.
I reinstalled the latest versions of eclipse/myeclipse/BEA workshop for struts
and now things are not working well.
Right clicking  on the navigator and package explorer in the different perspectives ( JAVA, MyEclipse, BEA workshop studio does not always work 
To reproduce the problem install Eclipse 3.2 then MyEclispe version 20061111-5.1.0-GA , then BEA JSP workshop studio – trial  version 3.3 . Try  and right click on an item in the navigator and package explorer — change to different perspectives –JAVA, MYEclipse , BEA Workshop for Struts and try to right click again.
THen uninstall BEA Workshop for Struts. The problem goes away.
Hank