Did you measure your roughing bit and input that exact value for the diameter? I assume you are using a V-Bit for the detail pass. Did you specify the correct degree for that bit?
You are correct. Ruff cut is a 1/4 and detail is a 60. I did not measure but they are new. It did not do it on the plywood only when I switch to pine
It might be that the Z-Axis lost steps or something during the carve or you might not have set the Z-Zero for the V-Bit correctly prior to running the Detail Pass. If it carved correctly in plywood and then did not carve correctly in pine (and the depth difference is the same across the entire piece) the my money would be on the second option. If the depth issue got worse throughout the second carve then you are either losing steps in the motor or the Z-Axis pulley is slipping (if you do not have the pressed on ones).
With regards to measuring the bits, typically I only measure regular bits (good V-Bits are pretty good with respect to their angles matching specifications). I bet if you take a pair of calipers and measure the 0.25" bit it will not actually be 0.25"; it will probably be something like 0.245". This makes are difference when you are trying to make something dimensionally correct as well as when you are using Roughing & Detail carving. The difference may not seem like a lot, but if you are doing something like carving out a pocket for something to fit into and your 0.25" bit is actually 0.245" then your pocket will be 0.01" smaller on all sides (i.e. the 0.25" peg will not fit into the 0.245" hole). All that being said, the machine has a stated tolerance of 0.005" I believe, so take it as you will. The way I look at is that there’s no reason not to give it the best fighting chance it has at being exactly what I want.
It looks like you did not reset the z height for the v bit.