Just a note, it does say to disable your secondary display in the readme file that comes with the game, in case you haven't checked it yet. I've been doing it and the game runs fine (of course).
Not sure why it'd work this way unless at one point you put the Myst window on the secondary monitor. I know that any windows that I move to the secondary will always open on the secondary until I move them back. Does manually moving Myst onto the primary keep it on the primary for future openings or does it switch back to the secondary?
There are various glitches with using multi-displays which aren't necessarily program related (so I read in NVidia's driver release notes, for instance). Does the problem persist if you change your default display resolutions or settings? What happens if you switch the primary/secondary ordering of the monitors? Does the game switch to stay with the 'secondary' or does it stay on the same monitor regardless of whether it's primary or secondary?