Have you completed all the steps in these MOS docs?
How to find the correct version of JDeveloper to use with eBusiness Suite 11i or Release 12.x [ID 416708.1]
Configuring JDeveloper For Use With Oracle Applications 11i and R12 [ID 330236.1]
What Setup is Required to Create Custom JSP Pages to Run on the Ebusiness Suite 11i and R12+? [ID 884200.1]