Unless you are using time-gated curves, windowed to avoid room reflections, what you are picking up is speakers + room. In that case, unless your room is acoustically symmetrical across the spectrum (which never happens), some measured difference between the two speakers is virtually inevitable. And also totally okay. What matters is that the first-arrival sound be the same from both speakers, and you can't measure that without time gating, and even then you can't measure it down very low in frequency.
In particular, that 5 dB difference at 250 Hz is not the result of "a 2.5 inch difference in room placement". Your two speakers are much farther apart than that. The room starts to dominate below about 500 Hz, and from there on down each speaker interacts with the room somewhat differently.
None of this PRECLUDES the possibility of other factors being the cause of the issues you see, but they could just be normal room interactions.
Duke