Have you compared them in Hex editor? For example 046YF0G0.SRX from 2013.40 and 046YF0G0.SRX from 2013.41 are not the same ,even if size and name are the same.

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Files can have different MapId inside and wont work if it's not the same. This happens for example ,if you use NT JCV with NTU map and viceversa.