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I had not heard of major problems continuing from 1.03B, however it is always suggested to start a new game when installing a new version. i.e. finish or discard the current game before upgrading.

What's done is done though right. So as for what can be done about it now, I would say not much. Pretty much the only thing is to restore the game to the version you started the game under, finish the game, then upgrade.

What version did you upgrade from?
 
Yes compatiblity between versions varies.