We've just pushed an update that should fix issues with diagonal movement and with Ellen's movement in the final scenes. In our testing we have not found any problems with 1.00 save files. If anyone has further issues with this version, please do let us know either in the comments or on the Bug Reports board. Thanks so much for your patience and for your help with identifying some of these issues. It means a lot to us. =)
Cheers!
P.S.
Just to shed a little more light on this, the bugs were related to diagonal movement and how that interacted with save data from version 1.00. That's why this problem didn't occur in the Mac build (because that was newly released with 1.03).