I'm stumped. In an effort to explain my problem, this will be a long winded post. The machinist I have used for years and several engines has always been spot on. In fact, I don't even purchase bearings anymore, he has the correct bearings packed when I pick up the parts. I always check bearing clearance, early on, just with plastigage, but years ago I purchased a set of micrometers and a dial bore gauge, learned how to use them, and now rely on those measurements.
So now I'm measuring the main journals. I take 8 readings on each crankshaft main journal at different points, average the results for each journal, and zero the bore gauge to that value for each journal. One journal at a time, I clean everything, install the provided standard bearings and torque the caps to 70 lb-ft. On journals 1 - 4 I get readings right at .003. Main 5 comes in around .0035 with the oil pump torqued to 50 lb-ft.
So now I'm thinking if I put a set of .001 unders in the caps, I should be right where I want to be at .0025 on mains 1 -4 and at .003 on main 5. So I do that. Recheck everything and according to the bore gauge I'm right where I want to be. As one last cross check, I decide to plastigage each journal also. I install the crank dry, torque each cap 25 -50- 70, add the oil pump at 50. When I remove the caps the plastigage is really wide on each journal. Easily showing less than .002 clearance on each journal 1 -4 and right at .002 on number 5. I repeat the process. Same result.
I've never had this happen before and I don't understand why the readings are so different. The one thing I wonder about is how I install the caps. As it should be, the caps are an interference fit in the register. Right or wrong, I've always used a rubber mallet to seat the caps in the register. Could that hit on one side of the cap be smashing the plastigage?