@astro4000 It sounds like the guides on the Z gantry are out of whack. (technical term 
) As the guides are preset, maybe Andy or Chris can assist you in adjusting them if this is, in fact, the problem.
Yes, it is all about the guides with the lead screw being the centre pivot point.
Regardless of the cost or quality of the machine, there is no way to completely eliminate deflection in a machine that depends on so many moving parts. We went through the exercise last year - see previous series of posts - of figuring out how to stiffen the LM and listed things to do to minimize deflection and improve cut quality. 1) Make sure your Y axis rails are parallel to each other and perpendicular to the X axis. Early last year there were numerous posts on how to accurately square the LM. 2) Adjust the wheels so they turn by hand but are not too loose. Adjust the anti-backlash nuts so there is no slop in either direction. 3) Keep the router high in the clamp and the bit high in the router to reduce the moment arm between the cutter and the clamp. 4) Do critical work near the ends of the axes travel rather than the middle. This is obviously hard on large parts. 5) Keep feed rates, depth of cut, and stepover down. Choose between run time and quality. 6) Make sure the stock is flat and securely clamped down, especially thin stock. If your stock has a hump in the middle or the edges are not straight, it can move when cutting forces are applied. 7) Be sure to mic your endmills, and then test them with a calibration cycle at your typical parameters in the type of stock your use. It is not unusual, especially with small diameter mills, to find that they are smaller, or larger, than the listed size. It is also common to find that they cut as if they are a different size than you mic. Several us who have done aluminum milling discovered that the Sienci 0.125" mill cuts like a 0.118" mill. 8) Fasten you spoil board to the table and then face it and any temporary inserts you use on top of it. This will compensate for medium to gross misalignment in your LM. Check the flatness of your board in 3 directions with a straight edge. Don’t expect to get good results on jobs cut on a waste board that is not flat. 9) Start jobs on larger, maybe >8 or 10", stock with a facing step.
When the router is tight and tuned, you can tram, which is usually worthwhile depending on what kinds of jobs you do and how interested you are in good results. I make lots of small aluminum and brass parts where the benefits of tramming are less noticeable. If you make large signs and very small defects or thickness errors would be very hard to see, tramming might not be important. If you make thin parts, want super smooth surfaces, or want the best results possible just because, then tramming is helpful. If you face a piece of stock the size you normally cut and it is not flat in all 3 directions, length, width, and diagonally, the need for tramming is indicated.
Tramming is relatively straightforward. You are trying to to set the axis of the cutter, Z, perfectly perpendicular to both the X and Y axes, and keep it there while you move it all over a 30x30" area while forcing its way through the stock.
First make sure all the guide rails are parallel, perpendicular, and level. Level is the one most easily missed and the hardest to do. There were posts early last year while the Kickstarter machines were being assembled on how to do all these steps and it is described very well in the Sienci assembly instructions, but basically it goes like this: Make sure your table is stable and as flat as yo can make it. Since everything is based on the table, if it isn’t true you will never get a good tram. For X and Y, before the Y axis rails are screwed down, move the X axis rail to one end up against the stops. If you do this with the motors, make sure the jog speed on your sender is set low. Measure the distance between the rails, and set the rails at the opposite end the same distance apart. Screw the supports on the first end down. Move the X axis to the other end, making sure the rail moves smoothly. The Y axis rails may move slightly as the X axis rail travels, and if the X axis assembly is assembled correctly and tight, the X axis will be perpendicular to the Y. Bring the X axis back to midway and screw down the supports. Go back to the last end and screw the supports.
If X and Y are true, getting Z is easy. Assemble per the instructions. This should get the Z very close to where you want it. Check the router clamp to be sure the surface and edges against the router are smooth, and make sure the router body is clean and smooth. Make sure the router clamp is tight and all of the assembly fasteners are tight. To confirm the setup is good I found it easiest to put in a 1" face mill and face an 18x18" piece of securely clamped MDF with a big stepover. Do it a couple times. Check the surface with a straightedge and look for ridges in the surface. If there are ridges it means the Z is not perpendicular to the table. There are not too many adjustment points in the LM so you may have to shim. I put a very small, like 0.003", shim behind the router clamp. Is it perfect? No. Is it very, very close? Yes.
I hope this helps, even thought it was so long. Search previous posts on the forum and you will find a lot of people had similar questions. And please post your results, good or bad. If our common goal is learning how to do this better, the more info the better.
Stay safe. Have fun.
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Thank you BillKorn
Everything you say is all common sense.
I’ll leave the tramming alone for now as it doesn’t seem to be a big issue especially for small bits.
Just something I discovered.
I’ll have a closer look at the Z rails later. Just back from out of country and 14 day quarantine now.
Not a real vacation but more of a rescue mission being away from the house for one year and lightning damage repairs and the scratches and scars of my labours there to prove. Now it is ready for next visit whenever that may be.
Yeh, I can get longwinded.
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