Hi Hegartype,
The two main reasons that a different tool is cutting higher than it should (or lower) is because either the coordinate space is shifted on the machine, typically caused by the Z zero being off, and/or the machine losing position while cutting - which can happen if it plunges straight into material faster than the machine's Z-axis drive motor can handle powering through.
There's also the possibility that the first operation had its Z position offset while cutting, causing it to cut lower than it was supposed to.
The test is to zero your machine's Z origin and after running an operation jog the machine to a point that you know should be zeroed out (for any or all axes) and see if the tool is where it should be - especially after a roughing operation.
Depending on the machine, a 50% stepover for a 1/4" endmill can be quite a large bite to take, and I could see a machine losing steps downward, causing it to offset downward and cut lower than it's supposed to. I've seen this when roughing out a relief carving too quickly with a 1/4" ballnose cutter on a machine that had an underpowered Z-axis.
Let me know if you have any other questions or need help with anything else :]
- Charlie