Hey Eric,
So, the plywood base and LDF are going to be more susceptible to changes in humidity over the sealed plenum, which you've noticed. However, a lot of the success for these accurate depths are going to be dependent on making sure your vacuum is holding your plastic securely/evenly throughout the area you want to pocket. With plastics not being porous, I've always had good success holding them down with the bleeder & blower style vac tables. My question is if you feel like you have good hold down, and you zero to the top of your material and run a pocket, what sort of deviation are you getting when you measure depth of one area to another? Have you tried testing your z-zero on several spots of the piece before cutting? One thing to consider is that the thickness of the material may not be consistent throughout. Spindle tram is another, but I'm assuming you've covered that. I've had production runs like this before where the depth was important. Ideally, you'd be able to skip re-zeroing in between cuts since the work piece thickness SHOULD be identical, but in many cases isn't. In one instance, I found that re-zeroing to the top in between pieces gave me better consistency. It's something you could try. Overall though, in the best situations, I could keep around 5 to 10 thou difference between two pockets that were a foot or two apart on certain pieces but other times, it could be 40 or 50.
Matt DeVincentis
ReZurrection Control
ShopBot Controller Upgrades
mattdevincentis(at)gmail(dot)com