R# Ultimate and R# CLT do not find the same warnings

We are running the latest R# Ultimate 2017.3.2 on our development machines and also have a step in our TFS CI build that runs InspectCode from R# Command Line Tools 2017.3.2. R# Ultimate within Visual Studio reports several warnings (mostly "Possible 'System.NullReferenceException'") but the CLT on the build server is not identifying these warnings. I am having difficulty understanding why this difference exists.

We have a shared SolutionName.sln.DotSettings file I assume is being used, as evidenced by the fact that it obeys our excluded file list but doesn't exclude them when I use "--no-buildin-settings".

What might be causing these differences, and how can I better investigate them? Thanks.