This is really strange, I don't see anything like that myself macOS Sierra too - lines witch checkboxes are highlighted correctly for the cursor position for me.

A few questions:

1. Are you using multi-monitor setup? If so, does it happen with a single monitor setup too?
2. From the mailing list it seems you have the preferences window maximized - does the same problem appear when it's normal size?
3. In the mailing list you mention "Is it possible to disable the new dialog-boxes-are-tabs functionality?". The thing is there's nothing new like that (I actually don't understand what dialog-boxes-are-tabs means - yes, there are tabs used in the preferences dialog but it has always been like that). Is there some regression compared to previous releases (see http://download.geany.org if you want to test)?
4. "Pulling the tab out as a separate window resolves the issue." Hmm, how do you do that? Tabs cannot be dragged out from the preferences window as far as I know.

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