I'm having the exact same problem on my Moto x-pure edition since I upgraded to nougat and the new Google Assistant. One thing I can verify is that all my messages are being received even if I can't see them. I suspect this is a bug with nougat/the new Google Assistant/the new nougat messaging app.
I never had this problem on marshmallow with the old Google Assistant and marshmallow style messaging app. I wouldn't be too surprised if they fix it with an update eventually. They're in the process of completely overhauling the messenger service as I type this. If I find an answer in the meantime I'll let you
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