I also have sporadic trouble with copy/paste in nedit in latest sarge. I don't run Adobe Acrobat Reader. I'm logged in through ssh, start nedit from forwarded xterms. I don't think I've seen the problem with just a single nedit window open, but sometimes when I have multiple nedits (tabs / detached tabs / multiple command-line "nedit &"'s, it doesn't seem to matter) copy/paste stops working. I've just had the problem appear and disappear by doing nothing more than closing all nedits and opening some up again. A few times both copy and paste hung for a second or two, then didn't work; most of the time when this happens they don't hang but don't work.
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