midrange polarity? X-over 3 Pro

My first serious 3 way design.
Using Dayton's X-over 3 Pro software, while the normalized amplitude looks good, I noticed the Phase graph is poor. If I change the midrange polarity, and keep the tweeter and woofer normal the phase looks great - but sounds odd.

So has anyone heard of this before?
How reliable do you guys believe X-over 3 Pro is?

I will not be able to invest in a microphone and software for post build measurements.
Using formulas in "Speaker Building 201" for enclosure, seems straight forward from a "Theoretical" approach.

1" dome tweeter, 6" mid and 10" woofer - all Dayton audio.
Using second order APC crossover.

THOUGHTS??
John