Can you provide some additional information, such as the lenses that are being used? Also, have you replaced the focusing screen, or any of the seals? Is the prism fully seated? There can be a myriad of reasons, but the real proof would be in the images on film.
Thanks for the ansewer. I used Nikkors 50mm f1.4 AI, 35mm f2 AI, 135mm f2.8 AI and 50mm f1.8 AF and the results are the same. I bought it used so I don't if anything was changed. The focusing screen is a H2 type. I think the prism is fully seated but I don't know how to be sure.
The prism has two spring loaded buttons on the side of the prism which are pushed to the rear, and the prism then lifted straight up. This is pretty much a foolproof method, but I just wanted to put this on your checklist. You may want to try a different screen to determine if it's just a screen quirk, or a bigger problem.
Since you're using the H2 screen, I'm pointing you to a web site which has a PDF you can download. It's a great chart which shows the compatibility of various Nikon screens and their lenses. It looks as though the 35mm f/2 isn't listed, though.
I cannot locate him today. You mentioned that you dropped a type B screen in your rig. That one has no split image in it, making it more difficult two know that the scene is perfectly focused. Could it be that it is just difficult to ascertain focus?