workbee behaving as though surface is uneven

I’m cutting both profiles and area clearances (workbee 1500, carveco software). It’s a fairly small sheet of 3 mm ply (40 x 60 cm). In some areas it’s not touching the material, in others it’s plunging right in too far and ruining the job. According to the spirit level, all surfaces are flat and even. Is this a common one and is there a fix?