The towns have empty tiles on them, but they are really empty grass tiles and not just buildings which are not (correctly) drawn.
Usually one would expect to have them overgrown with houses indeed, but maybe the placement check fails for those tiles (for whatever reason, maybe too many similar houses nearby, maybe intentionally to keep a bit green inside cities and allow you to build bus stations, maybe placement restrictions on the houses and none which can fulfill the ones for the empty tiles, maybe another reason).
The savegame asks for
52453400 87E88EFA687F91CE44548E54DA55059F japanese_buildings-3.0/jpbuild.grf
Maybe that's different with the newer version, as kamnet suggests. Test that, but best ask in the Japanese NewGRF thread whether there are intentions or known issues behind it.