What could cause a periodic "freeze" with no memory or cpu spike?

I experience periodic pauses of various duration(aprox. 0.5 - 1.5 seconds) on two scenes in my project only in the standalone builds. In task manager I watched to see if there would be a correlating spike in cpu or memory usage but there was none. My guess would be it has to do with a loop in a script somewhere but I've tried disabling and refining most if not all of the scripts that are likely to contain anything like that.