I'd guess that there was some problem in creating the patched sh3.exe file. If the patches were not exactly correct, then anything in the entire program could be affected, not just the intended target of the patch. In that regard, it is different from a mod.
I suggest you remove the h.sie patched sh3.exe, reinstall the patches in a pristine sh3.exe (You DID save the original sh3.exe, as the instructions recommend, didn't you?), activate the patches according the h.sie's instructions, and try again. BlitzKreig was correct that h.sie's instructions are thorough and carefully written. But they must be followed exactly. Any small discrepancy can get you an unplayable game. So go back to your saved sh3.exe and try again.
If that doesn't work, your copy of the h.sie patcher may be corrupted. Try re-downloading the entire h.sie patcher.
If none of this works, I' recommend a complete uninstall. Remove all mods, uninstall SH3 using the Ubisoft uninstaller, delete any residual files, and run a registry cleaner. Then re-install SH3 and start over. Hopefully, that won't be necessary.
One thing I can assure you. The h.sie patch package does work and is used by many people successfully. The problem you encountered is somewhere in your system and is not a bug in h.sie's software. It will work for you.
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