Looking further down the buglist, I understand that Skim is using the system pdf renderer. So that would probably be Apple's, erm, "shortcoming", and outside your domain?
Graphics in scanned document render black
FTR, both preview and acrobat reader do not have this issue.
False alert about pdf attached note when opened from Netatalk volume
The command.c part of commit [9c355a] introduces a bug. It replaces the printf format...
It turned out that the time_t related entry was missing from config.h.in ... See...