So I made some testing. I decided to give it a shot and upgrade a little, within my budget.
Initialy:
Intel(R) Core™ i7-7700K CPU @ 4.20GHz
NVIDIA GeForce GTX 1060 3GB
RAM 2 x 8 GB
DirectX 11
This would happen:
One of the instances will be barely usable until viewed outside or undocked. Happening on all mixes of settings (including everything low/disabled, stopped updating previous post).
UPGRADE:
NVIDIA GeForce GTX 1060 3GB > NVIDIA GeForce GTX 1060 6GB
Same setup, same drivers, same settings.
Then i tested settings set all High, Youtube in front, multiple instances of chrome and some other small processes. In both cases GPU was not going into some kind of overdrive, both instances working smoothly. GPU used for upgrading was not new.
Later upgraded RAM to 24GB but no obvious difference observed.
SIDE NOTE:
While cleaning I damaged one of the RAM sticks. With downgrade 16GB > 8GB and 3GB VRAM the issue also was gone. Given RAM became a bottleneck and both instances were barely usable.