Combing on different settings causes different issues. I researched and found suggestions to the issues but in the end it turned out to be combing, I wanted to preface that by saying I've done various calibrations, confirmed my prints are accurate when measured and my flow rate is correct. I've tried several different retraction settings as well because I saw others with a similar issues and the common suggestion was retraction.
I have a Prusa i3 MK2 build with nearly all the same parts except a RAMPS 1.4 board.
Since I mentioned retraction its at 2mm 40mm speed. Print speed is 45mm.
When I toggle combing all I get lots of surface artifacts and very poor print quality
When I toggle infill only I get some areas that fail to extrude near the start of the extrusion on a layer
If I toggle avoid printed parts there doesn't seem to be much of a difference
If I toggle the setting off the prints look great however I have some larger prints which require a high percentage of infill and as you know this process would raise exponentially in time
I tried to take the best pictures i could, the prints dont look the greatest due to camera flash however the quality is quite good, less the issues. The anomalies appear during the same layers on each print.
Note on infill only When the X starts then about half up the X and again near the top, all on the left side of cube, this also happens on other sides but in different locations, within the slicer it appears these are layer starts. I have also played with my Acceleration and JD settings to see if that makes a difference and it does not. I have reasonable settings (900 Acc x .0444 JD) Have tried 400-700 Acceleration as well with other JD variables calculated based on a Jerk value of 8-10.