These images are the same geometry, using prusament default pla, 0.2 Layer, with the only change being the print profile - speed, structural, balanced.
What interests me is only the balanced visualisation shows a smooth actual flow rate and actual speed rate - and i see similar results when i print. 

If the visualisation is to be believed then the printer is speeding and slowing at random rates throughout the print creating defects.

I also see that when on balanced, and reducing the infill from 10 to below 5 % I get a sudden line across the actual flow rate, coinciding with the top of the next object.

The graphics are showing that the speed changes from 30mm /s  to 40mm/ sec at this boundary.  

I would love to hear what the dev's think about it - I dont think its only about visualisation, as the result is visible in the print.

The photo shows from left to right An early print with seemingly wet filament on 0.28 draft, after dryring on 0.28 draft, and then on 0.2 Structural. The prints had no top layer, and 0% fill.

My solution so far is: 

- Clean the gears with a little copper brush. 
- Tighten the Idler screws in with 1/8 turn to give a bit more grip on the filament.
- Also I found out that the bowden tube was not going as was adviced here: https://help.prusa3d.com/guide/6-nextruder-assembly_849034#850678
But it went between the arm and the electric cables.
So that might have been contributed to the drag of the filament. 

Now test running with some flat models at the rear of the bed. 

On the most left back in the movie you see the damaged instance/model because of the extruder going over it without feeding. 
The clicks seem not to hard, but they were. 

https://www.youtube.com/watch?v=GoCGvVfBwxw

In my current state, the advanced filtration unit is removed. My nominal chamber temp setting is 35C. I'm printing Prusament PLA and PETG. The top vents are fully open. Lowering the bed and nozzle temps barely impact the heat break and chamber temp, but they do impact my print quality. My room is 73F with 31% Humidity.

Prusa specifically marketed this printer saying that you could print PETG and PLA with the door closed, but I'm starting to wonder if that's valid.

I would love some advice.

I also created a custom filament in PrusaSlicer 2.9.5 called "Ambrosia GenPHA" that's based on ColorFabb allPHA. In the Filament Properties of the Advanced tab, I changed the Filament type field to "PHA" by typing that in manually rather than selecting from the drop-down box. The Temperature fields in the Temperature section of the Filament tab are set to 150c Idle temperature, 195c First layer, and 200c Other layers.

In my printer's (not filament's) custom G-code, I changed the M109 line from:

M109 R{((filament_notes=~/.*MBL160.*/) ? 160 : (filament_notes=~/.*HT_MBL10.*/) ? (first_layer_temperature - 10) : (filament_type == "PC" or filament_type == "PA") ? (first_layer_temperature - 25) : (filament_type == "FLEX") ? 210 : 170)} ; wait for temp

to:

M109 R{((filament_notes=~/.*MBL160.*/) ? 160 : (filament_notes=~/.*HT_MBL10.*/) ? (first_layer_temperature - 10) : (filament_type == "PC" or filament_type == "PA") ? (first_layer_temperature - 25) : (filament_type == "FLEX") ? 210 : (filament_type == "PHA") ? 150 : 170)} ; wait for temp

Note the added alternative near the end that specifically mentions an initial nozzle temp of 150 if filament type is PHA.

None of this works, though. The printer still warms up the nozzle to 170c for bed probing, which is causing annoying material dots at every probing location that are difficult to remove. I just want the nozzle probing temperature to be 150c when PHA is the filament type. Why isn't my solution working? How do I accomplish that reliably?

I'm aware that I could create a printer profile specifically for PHA that would set M109 R150 as the startup G-code, but I'm trying to minimize the number of custom PHA-related profiles I need to select when printing with this filament. I would like to only have to choose the filament type and not a custom PHA print settings profile AND printer profile in addition to that. It seems like the M109 line in the Printer Start G-code is written specifically to accommodate this for different filament types, so I'm not sure why I couldn't adapt it to include one more filament type.

After printing with Prusament PLA for a while, the filament stops extruding. Only a few layers are printed. Then the gearbox starts making a clicking noise.
I’ve had to clean the idler and nozzle before (the filament hardened and broke). The filament feeding issue keeps recurring.
When assembling the hotend with the nozzle, the hotend moves around the axis (not just down); could that also be the cause of the problem? Thanks 

I just wanted to ask, if your printer also smells like burning acrylic. I had my first C1L shipped about 2 months ago. Initially was everything okay, but after around 2 weeks it started to smell horribly  It was also throwing "AC link lost" faults and ruining my expensive prints from nylon. So i returned this printer to Prusa. They've send me a replacement printer (that was nice from them). Everything was okay, but now the same horrendous smell has appeared on this new printer after just 1 week. I have a feeling, that it needs to be a "feature" of all the C1L. I highly suspect the orange insulation under the heated bed. I print only nylon, so the heated bed is all the time around 115 C and chamber 60C.

I am really sad, that i have to go through this. I love the print quality (just awesome), but these things just bother me and i even had thoughts about going the different route... I cannot sit near my printer, it smells really bad and toxic. 

Is there anyone else, who prints from higher temp filaments and having this issue?