GregValiant 1,342
As Geert mentions, your extrusions aren't welding to the adjacent stripes allowing a view of the layer below and unless it's a "look" you were going for, you are still under-extruding but what looks like a lot.
If the higher layers are coming out good I'd kick the flow up further on the early layers. Go to 150% and see what it looks like. You could manually step the flow back down using M221 S??? at the start of the first three or four layers until you got back down to 100%. Custom machines often need custom touches.
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geert_2 558
I am just guessing here, so...
The wavy aspect looks like the previous lines shining through. Thus: smooth previous lines will show through less than lines with big gaps.
Have you checked if layer-height, speed, temp and cooling fans are the same everywhere, on all layers? Often they differ for the first layer(s). If they are all the same, I would guess that the bed is too close. At least if it would be a standard 3D-printer; hard to say about a custom one. I don't know if effects of pellets not molten enough might play?
Long ago we had a plastic company in our neighbourhood: they extruded pellets into lollypop straws. Each time they started up the machine, after warming up, they had to extrude and waste some material, before the flow was steady enough for production. I could imagine that you have similar startup effects at the beginning of each print: different temperature and viscosity of the melt? If you can, try manually purging some material, and then immediately start the print? It could help diagnose things?
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