I don't really have any answers for you, so I'll just use your question as a jumping off point for a good rant.
Mixed messages? Are you kidding me? I mean, seriously people, this is HR 101. You must have a leave policy in place. It should contain, at minimum, the following information:
See, that's not so hard, right?
I mean, geesh, does HR think that no one is going to get sick? (Because that NEVER happens, right?) They should have a policy and every HR person in the company should be able to spout it out to you, consistently and clearly. (Okay, not every HR person. I don't think the HRIS people should have to know--strike that, of course they should, as they control the system that indicates whether someone is active or on leave. ALL HR PEOPLE SHOULD KNOW THIS. Well, maybe compensation...)
If you don't have a policy, managers are left not knowing what to do. Then managers have to wing it. Then Manager A wings it differently than Manager B and Bob gets great leave at full pay and Maria gets terminated as soon as FMLA expires and she didn't get paid during that time frame either. What happens when Bob and Maria (I'm feeling reminiscent of Sesame Street right now) run into each other in the grocery store? (Oh Bob is a person in your neighborhood, in your neighborhood, in your neigh-bor-hood!)
Bob: Oh, Maria, I heard you were sick. Me too. I've had these persistent migraines. I'm so thankful that I'm still getting paid.
Maria: What?!?!!??! (then a few chosen expletives, which I won't write because I don't say such words.)
Bob: What are you so upset about?
Maria: I haven't gotten a check in 4 months and they terminated me 4 weeks ago.
Bob: That's strange, I've been out longer than you have.
Maria: Excuse me, I have to go call my attorney.
Is this what you want happening? No. No, you don't.
Now, my real guess is that there is a policy, it's just that your HR department is unorganized and inconsistent. Escalate this issue. Get your boss involved. There should be clear guidance. This should not be an area for manager discretion.