Sorry for new issue, but I couldn't comment on my original post, since te issue is now "closed".
I totally agree with you that this could be some settings issue, but I none of mh attempts to "scale" pdf file in the right way in skim were successful. While both Preview and Skim are using the same engine, Preview differently interpret scaling (shrinking towards the center vs. shrinking towards the bottom left), as well as there is a simple option in Preview to set custom scale level in percents.
I would be very happy if youcan suggest where exactly should I look for an option to adjust scaling in Skim. I have crawled all available options and none of them were working, so I resorted to print out te document in Preview (so sad...). If it would help, I can provide screenshots/document that I'm printing out or anything else that could be useful.
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