I’d like to continue this quest because I don’t think I simply got lucky and everything just worked; There must be something to the setup.
My setup consists of VmWare: 12.5.2 build-4638234. I have a Win7 as host and installed Debian in VMWare using: http://cdimage.debian.org/debian-cd/current/amd64/iso-cd/debian-8.7.1-amd64-netinst.iso From there I installed using Joe’s script: https://github.com/jprochazka/adsb-receiver after a simple apt-get update/upgrade.
I dedicated 4 cores to the VM along with 4GB Ram, rest using default, No other changes. I used a USB extension cable plugged into the back of a USB 2.0 port on the back of the motherboard which contained a ferrite core (near the host PC). USB cable plugged into an RTL-SDR v3 dongle. I ran said setup straight through an FA filter with 25 feet of RG-6 to an FA 26" antenna. MLAT worked like a champ without issue for about 3 weeks solid, no other tweaks (I installed dump1090 mutability through the script).
Would be good to get to the bottom of this for others that maybe looking at using VM instead of Pi.