It is not enough to simply "flatten" the PCB. No matter how you mount it, the height variations will still be enough to spoil the traces and/or break the bit.
You need some way to ensure the constant depth of cut - either a depth ring, or surface probing. AutoLeveller is the program many people successfully use.
Spindle runout is also critical. It does not take much runout to spoil the cut and/or break the tool tip. Many entry-level "spindles" - DC motors with ER11 chucks slapped on - are nowhere near accurate enough for repeatable PCB milling.
Also, a homebrewed machine with limited rigidity may require VERY conservative feeds and speeds. My current settings are 4000RPM and 100mm/min, for instance.