We had a similar issue here once and found out that we were using a mold release on the back side of the part that was affecting the front (carried over from fingers or fixtures most likely).  Also, check the manufacturing process.  People sometimes find what they think is an easier way to do something that ends up adversely affecting downstream processes.  It wouldn't surprise me to find out you've already done these checks, so I hope you find the cause.  Problems like these never seem to go away.

Some amine-adduct cured epoxy coatings can produce a by-product from the curing reaction over time.  It usually looks like someone put a thin film of olive oil on the surface and can be blotchy.  You do not say what the epoxy is - they're usually polyamide epoxies in intermediate coats in the type of system you describe.  

I wonder if this could be either physically affecting the PU or could have caused a reaction with the urethane when it was applied that compromised the cure and it is the affected PU that you're now experiencing.  

Along the lines of "One test is worth a 1000 opinions"  good FTIR analysis and SEM examination(replicated as needed)of the "blotchy" and "unaffected" areas and even an "ideal" sample should help your investigation.