Maybe your speakers are very directional. If so, and the toe-in isn't symmetrical, it could show up as an issue in the measurements. AFAIK, you probably want to do a gated sweep if you really want to see the speakers performance without room effects for troubleshooting purposes. The subs actually look great except for the peak. Since those are sealed subs and I'm assuming no weird EQ shenanigans, that has to be a room mode, not a sub design issue.