I found the only way to get this to effectively work was to
a) Do not update AOIA to the new items database when you start it - some things have been renamed and will cause the compare to fail.
b) put both exports in the same folder as the script so you don't need to include directories
c) put a single quite (") in front of the AO prefs directory, but none on the end, this will help the argv parser preserve the end \
ie:
php merge.php PRE.csv POST.csv "C:\Users\<your account name>\AppData\Local\Funcom\Anarchy Online\fee9508\Anarchy Online\Prefs\<AO account name>\Char<new char ID>\