So I decided to resurface my bed from heavy use.
Following the resurface, I remeasured the spoilboard height (Calibrated the work surface height) and then zerod the plywood I was going to cut. I know the plywood is 0.49 inches in thickness but the Z height says it is 0.53 and when measured again was 0.56. What could be causing this? The bit is in the collet tight but something isnt adding up. Thoughts? Thanks!
Are you measuring the same spot as the machine? Plywood, like MDF, is not uniform in thickness.
(Ask me how I know. 
)
Yeah I get that from the 0.53 to 0.56 but even running the toolpath I am digging into my spoilboard.
I did have the gear rack start to vibrate loose in a few spots. Litterly the vibrations were backing out the bolts holding the two pieces together. So I had to put it off and tighten and place back. This occurred after the surfacing. Just not sure if this could also be related?
This is very true
Absolutely. Get that sorted out and try again to see if you get consistent results.
Just to circle back on this one. It was definitely the gear rack coming loose! We’ve added that into our maintenance check schedule!
You can always use a dab of blue loctite on bolts to keep them from vibrating out.
At what point do we do this for every bolt on the machine? 
There’s no real harm in using the blue stuff. It’ll hold things in place but it will still let you take them out should you need to. We don’t recommend against it, but don’t tell people they need to just because it’s not something we see as a recurring issue… However since these aren’t factory assembled so everyone assembles them a little differently and uses them a little differently.
You want to be careful on some bolts, like those ones that hold the Z axis to the back plate of the gantry, they can strip out if they’re in too tight (ask me how I know) 
Those 10 little 5 mm screws are a beaner too! 
Just replace them after you take those out..
I learned this the hard way too. Not only is plywood not uniform in thickness, I’ve found that especially with the thinner products (like 9mm baltic birch), even if its thickness is relatively uniform, its flatness might not be. If youre doing something where a couple of 10 thou makes a difference you could run in to problems. Like tabs for instance. I have had some batches of this material where it’s not enough to just use hold downs to keep in place and flatten the minor warpage acrodd the sheet because there are often “micro” warps that cause the topology of the material to vary by as much as .05” over relatively small areas (like less than 12”). This happens for me where some profiles with tabs that otherwise always work, don’t work on a given sheet. Not saying I think this is whats causing the issue in the post - just sharing. Maybe this is my CNC therapy group! 