I have the same problem: Most icons in the Calibre UI have become huge.
See the following screenshot for more details:
https://picload.org/image/rddaaodi/calibre.png
Toolbar icon size is set to "medium". Note also the oversized UI elements in the tag browser and at the bottom.
Calibre version is 2.68, running on Arch Linux x86_64 (Gnome). I also tried the latest git revision. No other program shows these issues. DPI and accessibility settings are all normal.
Any help is appreciated!
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EDIT:
This is apparently the same issue as Grollicus had with the ebook viewer:
https://www.mobileread.com/forums/sho...d.php?t=278442
His solution worked for me as well.
As the comments in __init__.py already suggest, it would probably be best to create an option in the preferences to control the DPI scaling.
Keep up the good work, Kovid!