Don't quote me on it, but I believe it has to do with Maine's "Good Moral Character" clause. Many Shall Issue states do not mention an equivalent to "Good Moral Character" and Maine requires the reciprocal state to be the same or stricter than it's own laws regarding permits.
That's probably correct. Florida and Missouri permits aren't honored in Maine for probably the same reason that Tennessee's permit is honored in
EVERY state that honors any out-of-state permits...except Maine. This is despite the fact that our requirements are, in general, much stricter, even though we honor all out-of-state permits. In Tennessee, the permit applicant must be 21 or older, be a resident of Tennessee, take an 8 hour class that requires passing both a written and live-fire range test, and undergo a fingerprint-based background check. Maine grants permits to persons age 18-20 and doesn't require residency (I'm not sure about their requirements regarding the class and/or fingerprinting, if any). Heck, even Nevada, Minnesota, and more recently, Washington State recognize our permits; and those are probably also in the top 5 hardest states in which to earn reciprocity.
Unfortunately, despite how strict we are, our permit doesn't ask for or check the applicants "good moral character." Our disqualifiers for permit denial more or less match the Federal prohibitions against firearm ownership, plus a couple of extra ones (for example, an applicant can't have a DUI record within the last five years). Our disqualifiers are pretty black and white: either the applicant is eligible or not eligible. There is no "well, there's nothing to prohibit you from owning a firearm; but I'm not sure about your moral character; permit denied." Perhaps the "moral character" clause is something the Maine legislature should consider removing, especially since it gives the licensing authority the ability to capriciously deny permits based on subjective criteria.