First of all, MKV it's just a container. Like AVI, MP4.....To decode audio and video streams, same filters are used, nomatter which container it's used.
Did you install AC3Filter as system or just local (codecmanager) ?
See the attached photo. I have installed AC2Filter as system and it's working fine.
There seems to be another fix for that issue. Go to LAV Audio decoder properties, mixing tab, and enable mixing. Seems to fix the problem.
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