I will send some files to you today but honestly I don't think that this belongs to the files. I use Media Encoder 5.5 and tried with several codecs and in 4.1.11 everything works perfect.
My opinion is that something changed in the audio rendering code in 4.2, or the new dxv osx preview plugin cause this strange behavior in some specific cases.
Or just hackintosh can not manage this tiny details in the audio codecs. I hope that I will upgrade to 1.8.5 today so I will let you know if anything changes.
Mainly same hardware - only GTX 680 changed to GTX Titan X - but 10.8.3 upgraded to 10.10.3 and the problem disappeared. Res 4.2 timeline mode works as expected.