Alright, After messing with it for days I have finally figured out what was happening. No matter what I did on Windows 10 I could not get the exe to patch.
I installed SH5 on my laptop which is running Windows 8.1 and tried it there. It gave me the same error at first but I realized I forgot to close steam. Upon closing steam it worked flawlessly. I then copied that exe over to my Windows 10 Desktop and tried the patcher on the already patched exe and it worked perfectly.
It seems that the patcher can't start with a clean unpatched exe on Windows 10 but once the exe has been patched you can use the patcher to activate and deactivate patches as needed. I went through as tested it on windows 10 by enabling and disabling the intro movies several times to make sure before coming here to post my results.
Hopefully this will help any newer or returning players that have the steam version on Windows 10.
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