Unaccounted Time between UpdateSceneIfNeeded and GPUProfiler.EndQueries

I have noticed a large amount of these Unaccounted Time issues, but I had not found any posts for the combination that I have. That is between UpdateSceneIfNeeded and GPUProfiler.EndQueries, and it is always right on top of the CPU Usage in the Profiler, taking up 96+ % of the usage.

I am using Unity 5.5.0f3, I came across this when I was trying to find why I am barely reaching 20fps. It looks like it might be tied with the Profiler running, but I am not positive. Does anyone know what would cause this Unaccounted Time, and how to fix it?