Is it the Drill Report that's telling you about the holes?

Or the DRC?

What does the Hole Size Editor Tool list as holes? Anything odd?

Can you locate a zero sized hole on the board from data in the 
Text Drill File?  One thing to try is to select all zero holes and attempt a 
global change to, say, 100mil; that can help you to visualize what's going
on. 
(Of course, you'll have to deselect SMD pads and other "good" zero-holes.)

It may be that you somehow wound up with zero diameter holes on
a mechanical or drill drawing or keepout layer. I think the drill generator
will 
output data for any holes on all layers, whether they are visible or not. 
Make sure All Used Layers are turned on for display.

Try to repair the database using the tool under the green "down arrow"
in the upper left of the toolbar area. You have to close the .ddb
before you can repair it.

Good luck....


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