I've discussed this issue with Peter and has been added to the bug list, but just to make other Users are aware of a potential (costly) error.
When Plotting & Printing, make sure that the "Device Setup" parameters for drill data minimum drill size is consistent with your design. If the design has a 0.4mm hole and the minimum drill size in "Device Setup" is set to 1mm (say) then the pad will be drilled @ 1mm, potentially drilling away the annulus of the pad as well! No warning message is flagged up informing the designer that the drill size has been overwritten with a larger size.
Ah.... so it will only really affect slotted holes, I did wonder as mine is set to 25 thou, and of course we use via holes a lot smaller than that and never had a problem.