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I like the fact that all my windows come back where they were so I dont shut down my programs when I turn off my mac. I find that on reboot some programs have shadow windows, like two instances but while one works normally the other is frozen, slightly greyed out with a spinner in the middle.

Shutting down the program gets rid of the copy but I would like to know if this has a negative effect on my system and if there is an alternate solution to get rid of them? Also is the fact that I dont shut down programs the culprit and should I? If I do, how can I get them to reload How they were?

Thanks in advance for any info you can provide :)

Edit: Programs I have experienced this with include text wrangler, Adobe Illustrator Chrome to name a few If I get 10 rep before this is answered I will post a screen shot :).

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Could you name the programs that show this behavior? Is the problem reproducible, that is, does it always happen after starting your Mac, or only from time to time? If the program you are referring to is a web browser, do the "shadow" windows have plugins (like Flash or Java)? –  jaume Feb 13 '13 at 14:09
    
@jaume I have edited my post. The shadow windows look like a shaded version of the normal program, but if I have six files open in text wrangler the copy will be empty. –  Totoro Feb 13 '13 at 14:28

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