Sorry I was too quick to reply and didn't completely read what you wrote..
This scrolling behavior is part of the OS and is OS dependent. Prior to FlashFXP supporting groups, large site list were a problem, similiar to the problem you face with site bookmarks. To solve the problem an option was added to force the menu to break every X items. This feature was added to each menu.
As time went on this feature was depreciated and forgotten. When site bookmarks were added this feature was neglected and not provided. I will activate it for the next build.
My second suggestion was for the sites menu. I didn't realize you were specifically referring to the site bookmark menu.
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