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I am having this problem as well, where Calibre appears to not save preference changes or window resizing. Running OS X 10.10.2, Calibre 2.20. I think it was happening for me in at least 2.19 and maybe 2.18 as well, but just didn't pay much attention because the only symptom was that the window size was maximized without manually changing it.
I tried backing up my old gui.py and gui.json in ~/Library/Preferences/calibre. Calibre created new files, but again would not save changes after that once I made them. I checked that I have read/write permissions on these files as well and also tried rebuilding permissions with Disk Utility.
No luck with any of this.
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