There is a bug with elevated maglev ways. See attachment (taken from japanese forum).
In order to fix the bugs, all the pillars have to be moved to the front of a tile. See second attachment: green - fine pillar position, red - bug causing one.
Anybody wants to give it a try?
Sources are available here:
http://simutrans.svn.sourceforge.net/viewvc/simutrans/pak64/way/
see maglev.dat.