Is this a phase issue? How to fix?

Place speakers close together and facing each other (a foot apart) and check phase by reversing leads on one speaker. When speakers are very close the phase issue will be obvious in a weakness in bass when out of phase.

If it is CONSISTENTLY poor through the bass it’s a polarity issue. If on the other hand, you see rippling of the frequency response at your seated position this kind of thing can happen because of different path lengths from the speakers to the microphone from different reflections.  You should notice not only dips but peaks as well.

+- 5 dB is definitely in the range of the latter issue. Polarity issues are usually wide and deep.

Are you measuring the levels from the same position in the room? I.e., at the listening position, for example?

The woofer in one speaker may have accidentally been hooked up in reversed polarity. Reverse the connections on one speaker, and measure again. If there is now more bass, you have your answer. The question then becomes, is the entire speaker reversed (all drivers), or just the woofer? If only the woofer is connected in reverse polarity, swapping the internal black and red leads on the woofer will correct the situation. If it’s the entire speaker that is in reverse polarity, swap the internal leads on the speaker’s binding posts (permanent fix/solution), or the two leads of the speaker cable on the exterior of the binding posts (temporary).