I too had this issue, since upgrading from RAD 7.004 to RAD 7.005.
Steps:
-I exported the ear file in RAD,
-Checked the ear file and it contained the correct classes etc,
-Deployed it to WAS 6.1 and it deployed ok,
but when you open the homepage [or any page of the app] get class not found, and on checked the expanded ear folder in the tmp dir the class files are missing.
I logged a PRM with IBM and they said it was fixed in RAD 7.007, I've recently upgraded to RAD 7.5, and due
test and confirm it's fixed.