Found the issue and fixed it. There were some extra entries in the default pjsip profile which were the culprit. The entries were there since quite a few versions back and hadn't caused any sort of issue with the trunks until we updated yesterday. Even after reverting to the previous working version, the trunks wouldn't get properly created until I found the extra entries and removed them. After that, the endpoints are created and the trunks are up once again.