I forgot all about Stainless saying he had the 4 die Lee set. Yes the LFCD will swage down cast bullets. I ran into that problem with the 45 Colt and 357 Magnum. Casts were being swaged down .0015-.0020 below what I wanted to shoot. My solution was to remove the carbide ring and the problem was solved.I can almost guarantee that the LFCD, the 4th die, is the culprit
So far from what I have read, you have seated a .4015 sized bullet after using the sizing and expander die on the case, then pulled the bullet and got a reading of .401-.4015. But, when you follow up with crimping the bullet with the LFCD and then pull the bullet, you get readings of .398-.399.
I think fredj338 may have hit on your problem. However, as geargnasher has said, take it one step at a time or you'll never figure out the real problem. You're getting a lot of good advise on here but it can be confusing. I thought the problem might be the expander die but now I'm leaning towards the LFCD.