First off, is your copy of SH3 already patched to 1.4b direct from the DVD? It most likely is if it's fairly new.
Secondly, if the patcher is complaining about help.txt files only, just delete them from your SH3 1.0 install. The patcher will replace them after it completes (note this is not the ideal way but it will 'fool' the patcher into working).
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