"Silence Selected Clips in Time Selection" working erratically in Audition CC for OS X

I am working on a multitrack audio file and using the "Silence Selected Clips in Time Selection" to quiet any background noise between pauses. 60-75% or the time it's working fine but the other 25-40% of the time it reacts in a super odd way and takes all of the markers it makes down to -∞ db and I have to fix it myself. I also should note that I am using Synergy to share the keyboard and mouse across screens (in case it is a stuck key issue or something). What is causing this, is it something I can fix?

I have tried it in both Windows 7 and OS X and with and without the mouse sharing software, and with snapping both on and off. Maybe of note is that there are parts that I have silenced and then cut out part of after the fact, I'm not sure if that would affect it or not. Also, just in case it wasn't clear, I am doing this in multitrack view. Here's an example of some of the cuts:

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"Silence Selected Clips in Time Selection" working erratically in Audition CC for OS X

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