Thanks, I have never bothered to test it until this time, but now I set a notification with only a sound and Messenger started to behave strangely. As you said it doesn't update the contacts' online status even if Plus! notifies for them but this happens half of the time. The other half of the time, things are normal. Messenger showed the signin toast as soon as I heard the Plus!'s notification sound.
Also, for one contact, it notified me about he signed in when he changed his status to Idle in fact (I know he signed in much before thanks to Plus!'s notification and at the moment Messenger notified me he signed in, Plus!'s Event Viewer showed he changed his status to Idle, so I think it catched the signin case on the second event of that contact. I believe some workarounds are being done for this problem.
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