[Nyororin]

It is their full discretion, but they are likely to only be concerned if you give them a reason to be.
Basically, your situation is very far from being suspicious and isn`t that uncommon a pattern. Lots of people travel to Japan and then head on to another country (or the other way around).

If you, say, had been in and out of Japan 3 or 4 times in a short period of time, had done the Korea ferry multiple times, etc - basically the type of thing that made it look like you were living/working in Japan and violating your visa - they have the discretion to turn you away.

In your case, there isn`t much of anything suspicious, so I find it hard to imagine they will do much more than glance at your papers and stamp away.