After installing the Alternate Start mod, I've found many odd objects around the map.

They are transparent yellow rectangles jutting out of the ground. I'm thinking that these might be spawn points for Endless Warfare, but its odd that they would show up after I installed Alternate Start.

I'll test this out later, but in the meantime, does anyone know a possible way to fix this?

Fix your load order, make a Bashed Patch, toggle the Archive Invalidation are the typical things to do.

Ok, now I am frustrated with myself.

New forum rule: ignore every thread Waymer makes about a tech problem because he solves it every time by restarting the game.

As long as you got it fixed, that's all that's important.