X2D print quality issues

In the last days started to print actively and yesterday tried one prototype. It got horrible under extrusion in the first few layers. This is with brand new BL PLA Basic white, freshly calibrated both advance and rate! And of course this was playing on my nerves and I decided to try some stuff. Played around and reread some calibration and first layer fix topics. Looked in the menu and saw manual first layer calibration. Which give you the option to manually set the Z offset +/- 0.05. I have set it to -0.02 out of the blue and to give it a try. Then gave it a fresh low + high temp calibration, which seems to made a lot of calibrations like 2x times fast and 2x times slow with more precision. Then made a primitive cube 200x200x0.2 and started a print. It again did at least two bed calibrations, not sure why it did more then one, as I have just completed the calibration prior that. I have the auto bed calibration from the print menu at - ON. Then it printed absolutely perfect first layer, which has amazing adhesion between the layer lines, and to the plate! I am not sure if the -0.02 ( should be 10% from 0.2 layer) could make such a big difference, honestly I do not believe so. Or just because I have touched it, it did some internal reset/init, and this time it was able to calibrate properly?

I am try to figure out what was that?!?!?!?!

Currently reprinting the same prototype which had under extrusion on the first layers and it comes out great.

For the calibration for the flow rate I picked 0 patch, which is basically the default flow for PLA Basic - 0.98.

Lets see now how will be the top layer part. WOW