Odd issue when splitting stereo files..

One very useful feature in AA CS 5.5 is splitting stereo wavs into two mono files. I work in games developer and need this.
But an issue has arisen with a tool I use that converts to a particular format for Sony PSP games: it doesn't like these split files. It's fine with the stereo files and with other mono samples, but not the product of the "Split to Mono" function.
Does something happen to the .wavs when this is carried out; are they 'different' in some way? Opening them and using "Save As.." to create a new file solves the problem but it would be good to know why it's happening.
Jerry

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