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Is the case that BI Publisher does not see the projects right away, in real time, or does not see the projects after the scheduled job runs? You can see the jobs next run scheduled under Administration->Global Scheduled Services and it will tell you the status of the last ran jobs as well. The whole interaction with BI Publisher took me awhile to get but since then we're creating our own custom reports for management and the only time the developers complain about not seeing the new projects is when they have been added during the day (our jobs are still on the defaults of only running once per day at midnight).
See http://docs.oracle.com/cd/E25030_01/English/Install_and_Config/Admin_PDF_Library/connecting_bi_publisher_to_p6.pdf around page 37
You can try the below Doc at http://support.oracle.com. You need to have active Oracle support account for that
How To Refresh Publication Data In The P6 EPPM Extended Schema [ID 1415675.1]
P6 Project Data Is Not Being Published Via The Publication Services [ID 1333858.1]