One of my problems also.
TheDBA Manufacturing ERP / MRP package I have been implementing in phases suffers from some inflexibility. In this situation, the inflexibility is more often a benefit than a problem. This company never had a system before and operated off a conglomeration of Excel workbooks. The lack of flexibility in the new system, which is conceptually well founded, has allowed me to focus on discipline and the benefits of integrated non-redundant data instead of trying to work around the symptoms caused by lacks thereof. I would be surprised if JDE isn't more flexible with a lot more data being tracked than the DBA Manufacturing package I am working with.
That said, we are heavilly focused on engineering / design and manufacturing aircraft products, with significant ISO and AS9100 quality management and traceability needs, plus lots of pressure to compress design to cash cycle time and costs which complicates the problems.
I'm not complaining. Overall, it's actually quite a challenging and exciting environment.