No, no patching. After wracking my brain for a day or two I came to the conclusion that there was only one possible cause. In the folder for MoO3 I'd added a file named "Specials.txt". I still have no idea how that could be the cause but apparently it was...... So I've moved it to the desktop.
I used to have the same problem back in the early days, the patch fixed it for me.
Anyways, you can better download the patch and slam a mod on, go here to find some good mods:
You'll notice that the gameplay gets greatly enhanced after installing one of these.