The problem is now solved, it seems to be that hibernates parser does not 
support all that EJB-QL did previously. Most of the problems centered around 
using the AS keyword within a join:

SELECT DISTINCT OBJECT( p ) FROM Principal AS p, IN (p.roles) role AS r WHERE 
......

This worked in EJB 2.1 finder methods but does not deploy with EJB3 hibernate, 
should be:

SELECT DISTINCT OBJECT( p ) FROM Principal AS p, IN (p.roles) role  r WHERE 
......

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