First off, which version of pcb are you using?  Would you be willing
to try the CVS development version?

Have you read the pcb tutorial at http://www.delorie.com/pcb/docs/gs/ ?

Optimizing rats should be nearly instant, even for huge layouts.

Drawing a rectangle over the whole board is a common technique, but it
sounds like you have your layer stack wrong, so it's drawing on a
non-top layer.  That would confuse the pad-clearing logic.  Would you
mind posting your board at a point just before it did something
"wrong" so we could try to reproduce it?


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