I saw no problems on the one board "11" - everything with bottom side pads 
appeared to be on the bottom. But on "12" I saw what you're talking about. 
Then I generated a project library from it, and lo-and-behold about half of 
the components have their pads on the bottom. There are a few components 
which don't, and those have at least one instance on the PCB which is 
correct. So I speculate that sometime in the distant past you got some 
mangled components from somewhere, and just propogated the problems forward 
with copy-and-paste. You did, after all, mention that the problem only 
occured with designs where you had done extensive importing. I'd guess that 
most likely the origin was in changing the layer of the ref des, which used 
to confuse Protel severely about which layer a part was on.

As to fixing it, I don't see any handy way except to clean up the library, 
then reload the affected parts from the library and flip them to the bottom 
as needed.

Steve Hendrix

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