On both the forums he was a moderator of, these were the permissions (note: user group the moderator was put on has no special permissions that interfere with this)
For some weird reason, the member could moderate X forum (which he was already a moderator of) but had no moderation options/could not moderate on Z forum (which he was newly made moderator of).
After triple checking permissions, I deleted him as a moderator of both forums (effectively, deleting him as a moderator) and re-did the same steps to make him a moderator of both forums again, after doing this he could moderate on both forums.
It was weird, my first guess went that this moderator was first created on xF 1.1, so maybe adding another forum to this moderator messed the permissions up somehow, and re-creating the moderator seems to have fixed the issue. But I have no idea why this happened, I tried adding other moderators (who were made moderators while we were running 1.3) to additional forums, and they had no such problem (could moderate on all forums they were assigned as moderators), so this issue was isolated only to this one moderator.
I just thought I'd post this here, the problem is sorted out now (because I deleted the moderator that was having the problem and re-added them as moderator) but it was a weird incident.