After Effects importing wrong Illustrator file

I'm making a 2D simply animated film for my final year university project, where I'm designing in Illustrator and animating in After Effects.
This has worked fine until recently, but I've stumbled upon a problem. I'm creating my assets in groups based on my storyboards, and importing them one by one as I progress through the animation. They are all in the same folder and named 'Assets 1.ai' and so on. I have reached the 4th one of these files, but when I try to import it with the settings 'Composition - Retain Layer Sizes', AE brings in 'Assets 1' rather than 'Assets 4'. I've even tried this with the 'Footage' setting, which is useless to me anyway, and it still brings in the wrong file.
I can get around this by dragging the file from Finder straight into AE, but this makes all the layer sizes the entire size of the comp which means that I can't transfer any previous keyframes onto my new layers (I'm using several similar animations and layers) as they are a completely different size.
For example, a subtle rotation on the old layers of the correct size is a much more noticeable one on the new layers.
Does anyone know of a way to fix this?

It might help if we know some more information. Exact version number of AE (down to the last decimal), for example. FAQ: What information should I provide when asking questions?
What happens if you try to import it into a brand new project? If it works, until an answer is found, just import it into a new project and then import that project into your existing project.
Also, on a big project like this, please tell me you're using the Increment and Save feature with some frequency.

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