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).

Are you sure the DC was 5? The number that appears during the check is the number you need to beat to succeed, and is reduced by positive modifiers.

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.