I've seen that before as well. There's some kind of factor relating to this, and I don't know for certain what it is.
Maybe sysMMC and emuMMC have the same game updates installed in order to achieve this.
Maybe sysMMC stock OS and emuMMC CFW OS has to be at the same firmware version.
I've read that people don't know how, but suddenly the sysMMC and emuMMC profiles became split and was treated as 2 different profile, despite being originally same profile.
I can only imagine that a firmware update would cause such a split, since people update the emuMMC without paying much attention to their sysMMC,
but without concrete proof (and a way to test, since my SD card ain't big enough), I can't peddle that as fact now, can I? XD
It could be your router settings. My router could broadcast at 2 bandwidths, but I think my Switch can only connect to one of them.
But yeah, controlling the wi-fi using the phone as a hotspot may be an extra switch for you, tho it doesn't exactly stop your Switch, if it's holding a report and waiting for a connection.