Before I gave up on Word I found that I could copy/paste the fic from Word to a simple text program, set it to save it as 'plain text', then copy the plain text and paste it into AO3.

That seemed to have cut out the weirdness, but then I thought- I don't use anything in Word beyond what's in the simple text, so why not cut out the middleman?

If you use Word's features, naturally you don't want to give them up.