I was reading somewhere, I think it might have been practicalmachinist.com… I read that spindle runout increases with spindle speed. Which makes sense. If there’s any imbalance in the spindle, or chuck, or bit (and there always will be) increasing the speed will increase the radial force that imbalance exerts on the assembly. The feedrate is a function of spindle rotational speed (rpm) and lateral spindle movement speed (mm/min). If you half your spindle speed and… wait, did you say 5mm per minute? That’s lunacy. I think the default in my CAM processor is 80mm/min. That just makes me lean toward thermal involvement even more. Read up on pcb milling feedrates. I run mine at 40mm/min and get 0.015" traces. And my dewalt is set at half of max speed. The point is, reduce speed € reduce runout.
I just double-checked the feed rate and it’s in cm, not mm. So 50mm/min which is still somewhat slow but not totally crazy.
WHEW. That’s a relief! 
Did you notice that FlatCAM does everything with G01’s. Not an arc to be found anywhere… I guess I can understand why it’s necessary, since the software has to trace existing geometry and it doesn’t “know” the radius of arcs. It just makes for a lot of really tiny straight lines.
Better than Chilipeppr’s Eagle import function… It can’t handle arcs at all. It just slaps in a 45 degree angle straight trace somewhere. I made that mistake after designing a pretty complicated board with lots of concentric arcs, all pretty. Had to go back and redesign it or process in FlatCAM.
@MarkRichards
Have you cut anything successful with your new spindle?
I know it seems obvious, but some people have wired their DC spindle backwards causing it to spin in the wrong direction.
As for a 12K Spindle speed. I use my Makita at it’s lowest speed setting and its cuts fine. I think its lowest is around 10K.
Jeremy, what horizontal travel speed do you use at 10k rpm?
I have only used the default feed rate that pcb2gcode uses.
I’m back at the x-carve, trying to get to the point where I can consistently cut PCB’s. Now I can’t get the imania build to perform the Auto Leveling. It stops about 2/3 of the way through the process (the /grbl build doesn’t work at all). I have tried a half dozen times, with different files. It just stops. Here is a screen shot:
Do you have buttons hooked up to your feed hold / cycle start pins?
I’m guessing that is a no then. 
Mark, I was having the same issue for a while and it turned out to be that I had set the maximum probe/Z depth to be too shallow. I think it defaults to -0.5mm (or something like that) and in my case I changed it to -2.0.
I had the PCB placed in a milled out pocket in some hdpe, My issue turned out to be that there was a small lip at one end that exacerbated the angle of the PCB. Hence the -2.0mm Z requirement.
Once I fixed this, it was fine.
Thanks @CaptCrash, I will give that a shot! Sounds like a very plausible explanation for the issue I’m experiencing.
@MichaelUna: Do you have the g-code or gerber-file for your stress-test. I would like to do the test, too
A new tutorial I created on how to import Eagle BRD files into ChiliPeppr, generate your Gcode, and then auto-level your PCB before milling. Figured it would help the discussion.
Thank you so much for the advice on scaling the drills! I was going crazy trying to get that to work until I found your post.
You can now create solder mask Gcode in ChiliPeppr. It’s a new feature that X-Carve users might find super helpful.
If anyone has any ideas on what I’m doing wrong, I’d love some help. Started a new topic: Help with work Zero in Chileppr - #4 by ByronNeighbors