My boss likes to use "in that" when he really means "since." Is this acceptable? If not, what is the rule that I can tell him?
Since can be used in either a causative or temporal sense, whereas in that can only be used in the more causative sense (in that has other senses, but we are mostly concerned with where it overlaps with since).
In the causative sense, it is acceptable to say either I like X since it does Y or I like X in that it does Y. If you are unsure, try replacing since/in that with because; if the sentence still works, then you have the causative sense: e.g. I like X because it does Y, which still conveys the same meaning.
In the temporal sense, however, only since works. Thus, I have liked X since it did Y means I began to like X after it did Y. However, I have liked X in that it did Y means I have liked X because it did Y.
The lines are blurry and somewhat confusing. The main thing to remember is that, historically speaking, since is temporal and in that is causative. Since the days of yore their senses have been overlapping each other, however, and so I wouldn't be too surprised that the two are 'misused', so to speak.