This "All Mail" but not arriving in the In-box has been a problem with Gmail for many years. Unfortunately, the "simple" explanations posted above does NOT explain this phenomenon. I've been fighting it for years and finally decided that it was a major bug in GMail.
I finally implemented the work-around of adding filters which applied to particular "TO addresses" and did a "Never send it to Spam" on the "missing" email. (I had found that similar experiments with a filter for "Mark it as important" or "Categorize as Personal" did NOT help the situation.)
I do wish Google would fix this problem. It began to appear around 2010, if I recall.