To start, I would Re-Order the toolpaths, the perimeter cut should be done at the VERY last even if that means an extra toolchange. Doing this cut prior can cause un necessary movement of the wood (it might be more prone to lifting which could cause issues with depth, likely not this issue, but still… best practices…)
You’re right, the deeper portions are all at the beginning of the carve… you might have had a z zero issue to begin with making stuff deeper than it should be and then a bit slip back up in the collet OR belt skip a tooth while the Z is plunging down, resulting in the more shallow areas after the event.
IF you’re not doin so, its a good practice to remove the nut/collet and tap or blow out the sawdust. routinely and I suggest checking the belt tension on that Z axis.
Additionally when doing flat bottom pockets like this I like to set it up to do a thin final pass, this is done in Vectric in its own popup window and is pretty simple to setup. This is likely NOT the cause of the issue, but it’s a good practice in order to minimize the machine marks that are usually deeper from deep passes than from this thin last pass method.
Can you verify that he $1 is still set to 255 as well. It should be, but just as a sanity check, you might want to verify.
As for the Oramask method that I use:
I stain or paint, then apply a wipe on water based polyurethane, let that cure fully, for at least 1-2 hours. Then apply the oramask.
Then to cut it I start with the V bit doing a “score” cut using inside the line perimeter cut with a very shallow depth, like 0.3-0.5mm depth, just enough to slice the masking and a tiny bit into the workpiece.
then I swap bits to the endmill and run the carve as normal. By running the score cut I always end up with a very clean cut edge on the masking since it was adhered well and it was a solid piece, not already cut up by the endmill. using the endmill first makes it more prone to bunch up rather than slice it cleanly.
I hate to say it but I really think it’s going to be tough to clearly identify the root cause on that carve. only to check the Z belt tensioner, the pulleys are on tight (no loose set screws) and that the collet is clean and the bit fully tightened before each carve going forward. That’s about all I got 
it works perfect every time
Maybe you should create a new topic so it is easy for people to find that conversation. I know I’m hungry for all the tips I can get.