Source of this minor under extrusion?
I have 2 Prusa Mk3 printers, One prints fine and the other (the oldest one) is experiencing some minor under extrusion. It is better now that I thoroughly cleaned out the hotend, replaced the nozzle, adjusted the pin on the bondtech hear, lubed up the gears and just gave everything a good cleaning. I am still experiencing some minor under extrusion when printing fast top surface layers. I don't think it's my slicer profile, even though I could probably fix this by slowing down the print in problem areas. Something mechanical has to be causing this issue, I use the same profiles for both printers and have 10,000+ printing hours between the 2 of them. 
RE: Source of this minor under extrusion?
You can try to upgrade to the most recent firmware and do a factory reset. Sometimes the older EEPROM values are causing trouble. This is the first thing I would do.
Beside of that it's hard to tell. If the issue is resolved by just slowing it down (using same gcode), then either there is not enough pressure building up or the nozzle is colder. Changing thermistor might help in this case.
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RE: Source of this minor under extrusion?
Measure the extrusion length when commanding a 100 mm extrusion. Verify you get 100 mm movement from the extruder. Set multiplier accordingly. Also, measure filament diameter, and set it in the slicer. These two can cause what you are seeing.
RE: Source of this minor under extrusion?
@nikolai-r
Thanks! I have updated the firmware (forgot to add that) but I will try a factory reset and if that doesn't work I will swap the thermistor. I did already swap the heating element.
RE: Source of this minor under extrusion?
@tim-m30
Thanks! After I try a factory reset and possibly replace the thermistor I will take a look at this. Ultimately I would rather not have to make changes to my slicer profile to fix this. Currently, I am using the same profile for both my Mk3 printers and would like to keep it that way. Everything turns out fine, in general, its just parts with large top surface areas that are affected by this.