Seeking best practice advices for precision double side machining

The parts I makes typically requires double side machining and the Z thickness and flat over X-Y plane are two critical parameters.
I can measure my vice jaw flatness using Z probe over 4 corners as within 5~10um error. And there is tramming error that accounts <10um error over tip to tip in Y direction depending on the tool size. 
And here are my procedures to make the parts.
1. Create fixture on vice. Check flatness <10um variation corner to corner.
2. Prepare stock surfacing on vice on both sides
3. Does backside machining on vice
4. Flip and attach it to fixture on vice then front side machining
After this, typical error in thickness over corners are now in 100um range. I don't know where they are coming from and how to improve. My goal is to get to ~50um or less range.
Any advice would be welcomed.

Thanks
 

Could you post some pictures of your machine and an example completed work (just so we can see what exactly you are trying to achieve)?

Do you unclamp, flip, and then reclamp to machine on the other side?

It wouldn't have anything to do with jaw lift when tightening the vice ?
Does the fixture support the stock fully along the side that is contact or have you allowed for a "hollow" in the middle of the design of the part and fixture allows for this.