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Google wants to send users to sites that they want to find. And popunders are a big negative in most peoples book.
But I really do not think a sample of one site is enough to come to a conclusion. Losing a major incoming link could have the same affect.
I don't think Google is penalizing for this. As much as people hate the random popups/unders for the X10, Casinos, etc., targeted popups for things like newsletters many people don't mind at all (I boosted my signups by 40% when I added my popunder).
I think your lack of getting spidered fully is due to something else.
I don't think you have anything that would back up your clain though do you? Sites drop in and out of G all the time and pages get dropped and then re-indexed all the time.
With the amount of pages G has in its index funny stuff happens from time to time. I'd be willing to bet it has nothing whatsoever to do with pup unders and is either a glitch that will right itself in time or something is amiss at your end.
Hang in there, it'll most likely be fine again come next month...
Nick