This is something I noticed with the Necromancy of Thay checks, where I had a +3 modifier for the rolls but still failed. The most apparent was when I rolled a 2 for the first check (5) and should have passed. Not sure if this is more widespread but that was the first time I really noticed as it happened twice (may or may not have been save scumming).
Okay, so I checked again and Shadowheart has a +3 modifier and the first check to get is a 5, she was also the one I was using before. After that I used my own character who had a +1 modifier but the first check was a 9.