I had the exact same problem on a 1986 Kramer Paul Dean - Neck through body construction, Honduran Mahogany body wings, s/s/hum configuration, brazillian rosewood fingerboard. I tried everything to fix the problem (intonation, pickups - even EMGs, action, strings, technique, truss rod...). This was the flagship model at Kramer back the the day.
Sold the guitar and never looked back. Its the only guitar on which I could not get good artificial harmonics. I guess some guitars just don't ring the same way as others.