Our forum is building an app and we have developed a relatively complete and functional REST API for phpBB for it. However in beta testing we've discovered a perplexing bug. After someone uses the app and its REST API, PMs do not appear in his/her inbox for some time. These PMs may be sent via the forum, not the app. Interestingly however, they are still visible in the app (yet we haven't modified any phpBB code). Moreover, if I send a PM (using the forum) from another account of mine to my account that used the app and where PMs are invisible, suddenly all PMs that were previously invisible will show up in my inbox (on the forum).
If this post seems sparse on details it's because I don't even know where to look or how this could be happening.