Stacked pads refers to the situation when you have generated both a pad and a clearance in the same location. This usually happens when mid-layers 2 - 15 have a name beginning with the '$' character and both pads & vias have been generated.
If the layer name begins with the '$' character it is treated as a supply layer, always DESELECT both pads & vias when generating the Gerber files. You may also wish to check the Supply tab in the design rules. Restring should be deactivated for Annulus. If restring is activated for Annulus, a ring will be generated rather than a fully filled circle (pad).
This applies to versions earlier than EAGLE 6.0 as this has been fixed. If the board was designed in a version earlier that 6.0 and you open it in EAGLE 6.0 or later, you should run ratsnest to verify that all pads are still connected to their signals
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