Did you start with a clean and untouched sh5.exe or with a patched and then unpatched sh5.exe ? Since the patcher alters more then just the patches to the .exe, you should probably start with a fresh copy of all the files that are touched by the patcher, it adds stuff to different .act files. They have been altered by the previous patcher already I think. Possibly this causes the error.
For this reason, I'd install the patcher as a mod. To do this, copy the needed .act files together with sh5.exe into a folder where you unpacked the patcher. Run it from that folder, by pointing it at the files in that folder. Then install that folder as a mod using JSGME. That way you can always go back to untouched files
Did you back those files up ? If not, you'd have to reinstall I'm affraid.