I recently decided to install the game again and get that message every time I startup. I looked around and found this guide: http://nraas.wikispaces.com/Common+Install+Issues . I've done what they asked and I still have the problem. I've created a clean folder, and the problem persisted. I've run the super patcher, and the problem persisted. I certainly don't have anything in the (incredibly) old mod framework as I just installed this game and this computer is newer than that switch. I've even reinstalled and still have this problem, which seems to be a serious one based on the tone of that linked page. I'm at a loss as to where to go next.

If we can rule out core mod version mismatches (since you have no mods at all nor either kind of framework), Superpatching I presume to 1.67 was successful and not by running an older version of the SuperPatcher, and this computer has never "seen" TS3 before now, then I would have to say this is pretty unusual.

What is your source of install, it can't/shouldn't be Origin for Windows or Steam if we are talking about Superpatching, so I guess it's all retail disc or you are on a Mac? Possibly you have inadvertently run the 1.67 Superpatcher on a Steam or a 1.69 Origin install? Or is the install source from someplace else?

Disks, and its worked before. Albeit I don't think I ever got up to 1.67

And you are on Windows, not Mac? Is Origin involved in this install in any way or is it in any way trying to manage your game? The only way to stay on a pre-1.69 install is to leave Origin out of the picture entirely (on Windows, that is) and use a base game disc that was produced prior to Sept 2012.

If this is what you've got, is this the 1.67 SuperPatcher you are now using?
https://help.ea.com/en-tr/help/the-...3-super-patcher
(and ignore any "helpful" suggestions to use Origin to update that will appear)

Yes, I am on windows. No Origin isn't involved, and the launcher says 1.67. And Yes I'm using that superpatcher from that link.

Okay, well this is a known symptom of a broken installation but it doesn't mean things are necessarily broken. My inclination would be to uninstall everything related to TS3, clean the registry with CCleaner, and start over.
https://www.piriform.com/ccleaner

But I could understand not wanting to go through all of that again. You could also play forward though the warning if the game lets you dismiss it. There are users of core mods (Awesome, for example) on 1.69 or Steam who have to dismiss this warning on every startup and although the mod is not officially supported for them, it works out fine in many cases. The game might work well regardless, or it might collapse into a ball of fire after a couple of saves. Most likely the former, from the sound of it.