Problem : Customer noted that a Design that has over 50 source files containing package files will cause Project Navigator to write out _prj file that lists source codes from top level to bottom rather than from bottom to top. This will cause XST to error out. Customer has to manually edit the _prj and and save it as read only to bypass this problem.
Note: Customer can't send in design and I've no way to reproduce his problem. FAE wish for an investigation into this issue.
We have not seen this at the factory. Since the customer was unable to send in the design we cannot say exactly what is causing the parser ordering problem.
If a customer reports this problem, please get the design if possible