Should I award reputation for a quest if the PCs accept a reward?

I’m referring to the reputation system. In it, the PCs can gain reputation points for doing "favors" for groups. However, the rules aren’t really explicit on what constitutes a "favor".

If the PCs complete a quest for a group in exchange for a reward from that group (currency, items, land, etc.), can the quest also count as a favor? Or would the quest only count as a favor if the PCs don’t receive a reward?