Select pad properties (any pad, smd, tht, a mounting hole, copper heatsink, Kicad or personal libraries … anything)
Select a shape that allows both X & Y to be altered.
Instead of “right click” & “select all” on the pad size, place cursor at far right of the size and use the backspace to remove that number.
The right of the cursor in the X value remains empty, the right of the cursor in the Y value has one or two random numbers generated.
Select Hole, perform same experiment, same result with one or two random numbers generated.
If Hole shape is changed so Y value can also be altered, both X & Y have random numbers generated.
Same result with mounting holes and copper under ICs.
Please confirm before I open a bug report.
Edit: this is both 6.0.10 & 6.99