Definitely check out this thread for info regarding data that do not line up:

www.empirisoft.com/support/showthread.php?t=548

But with that said, it is true that a simple question wording change should have no impact on the structure of your data file. Can you send a zipped copy of your experiment folder (with data and all) so I can take a look at it? Send it to support@emp....com. If you also happen to have a copy of the folder from before you made the change that would also help.