InDesign treating a placed .ai file as a pdf

So this is a brand new MacBook Pro 15.1.1 (24B2091) with newly installed CC. 

I have multiple vector files placed that, upon export, come out really pixelated as if the links are missing (they're not). When I place them, this dialog box comes up as if I'm placing a pdf instead of an illustrator file. 
I tried resaving the vector files with "create pdf compatible file" unchecked, which had even worse results–no placed file that even displays in InDesign and just a message about how I should have saved it with the box checked. I've been using these programs a lot of years and haven't run into this before. I know the files are simple vector files and not raster, and all images are linked.