That makes sense. I never enabled Background Agents in the first place, then the IDE started throwing errors about the background agent not being able to find the git root.
I updated a separate 1.2.4 installation that had this issue to 1.3.5 (latest stable release) and when I disable Background Agents it does not turn it back on.
Could you please upgrade and confirm this is working for you? Otherwise let me know as well because this should not be happening.