Using the boat after summoning it from anywhere locks me in place and the party does not actually enter the boat. I've teleported to the 2 places I can summon the boat too, so it's not tied to any specific location for me.
Sadly, it's not just when you summon it. I did a little experimenting, and excepting the 1st boat ride to get down to the Royal Capital, the boat is completely inoperable. The very next time you see the boat is after you escape from prison and wake up in Neko Village. The boat is then waiting for you just north of town at the dock as soon as you regain control of your character, with no summoning necessary. Even then, it freezes game play.
Edit: It's also possible I got the "Cosmic Ray" treatment for my boats .... I'll do something extreme like delete and redownload the whole thing and start fresh, see if anything changes