just gonna throw it out there but not having full alignmnents have been linked to nominals changing. Not saying that this is your problem with the info provided but it may be something to look at. Maybe post the code.
You don't need to turn snap off in anything other than alignment points. Snap has no effect on nominal unless find nominal is turned on.
Always better safe than sorry I say. 99% of the time it serves no purpose for the task at hand, until that one time you find it's on when it shouldn't be
