Those boats are a bitch. I manage to avoid getting switched to the wrong boat by running forward. I've seen several bug reports filed but nothings been done to correct the problem. Don't know if they can fix it.
Boat from Qeynos to Erudin
*edit*
Maybe it is fixable. I noticed from your bug report that the boats were fine a few days ago...I guess the paths get messed up now and then. Maybe someone will reset the boats.