This happened to me on Mplayer CE (the previous app) while using libdvdnav, which is the default on WiiMC. A workaround would be to go into the options and set it to “Play first title” (as I remember it).
Edit: Forgot to mention that it re-synced after a minute or two into the new chapter. How good this is depends on how split up (into chapters) your DVD is.