Why preferences make a grafical bug when you close it?

[http://screencast.com/t/mosz2dXev Here can you see a video of the problem]
I have tried to disable all addons, but it did not help.

There are two reasons this happens.
1. The file is damaged, or (more often) made slightly wrong by bad software (more common than you'd think). Adobe Reader repairs the file, and wants you to save the repaired file. (If you do, the message won't be repeated)
2. The file does some clever stuff with forms when you open it, and changes the file. Again Adobe Reader wants to save it. (Even if you do, the same thing could happen next time).
If you didn't make the file you can safely ignore this.

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