Hi Jessica,
I'm trying to reproduce the issue in my env. but I can't see the behavior you see.
I have multiple doc libs from different site collections for which I have version and check in/out turned on.
I have no problems checking out docs, edit them, check them in the repeat the steps.
If I open directly the doc and try to edit, I'm asked by Word to check out the doc, I do that, then I edit then I check in the doc. I can repeat then the same steps and I don't get any messages saying that the cod is already checked out.
Can you please double check that what I'm doing is what you do. If your steps are differnt then please let me know the sequence so I can do the same.
Thanks,