I'm using MPD + IPv6 + MLPPP as well at home and I most definitely have it configured to use 1486 and never had any issues. I don't recommend using 1500...it might work but it's not proper.
Are you using MPD w/pfSense, roll-your-own, Tomato or other? I'm presently using pfSense with some hacks to make IPV6 work. In general pfSense seems good, but it has some quirks that annoy me. Looking for something better.
Using OpenWRT here works great.