I also filed this as a bug (https://youtrack.jetbrains.com/issue/TW-42257), but just in case anyone here knows how to troubleshoot this....
I have a project with about 17900 inspection warning, when run repeatedly on the same agent, on the same code revision, with "clean all files checked", the warning count is not stable, but goes up and down by a few 10s. New warnings are generally in files completely unrelated to the last few code changes.
The same issue existed in v8, an upgrade to v9.1 did not fix the issue.
I want to start failing builds based on the inspection count not going up, but if I can't trust the inspection count this is not possible.
Please let me know how I can troubleshoot this.