Since you are using the undersizing die, the i.d. of the case is being sized down .001 more than usual. The bullets you are using are coated so they vary more than jacketed and some are probably .401 dia.
If you aren't belling the case mouth enough the bullet may seat crooked in the case. That's why the marks on the case with the sharpie on it are opposite of each other.
I have this issue also when loading coated bullets with my 2011. I will get about 10 rejects out of 100. Now if I load Jacketed bullets or even plated, only about 3 or so fail the chamber test. All of them that fail work fine in my Glock G35 so I load at 1.135
These are some of the issues I have ran into while loading 40