I can only tell you that with both SHIII and SH1V, I only ever save at the map station, and I always rotate the saves between two files. In other words, I'll save to 'TDK1' and then about five minutes later I'll save to 'TDK2' and then back to 'TDK1' again five minutes after that.
This means that if there was some corruption/error with one of the saves, I can use the second save which will be within five minutes game play of the lost save.
I have never had a bad save or encountered a problem with either SHIII or SH1V using this method.
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