Beings you are renting, you're most likely not about to get any help from the landlord. He'll need to spend some $$$ to have the ENTIRE HVAC unit inspected, cleaned, and who-knows-what-else. I don't know your situation but there isn't anything preventing you from getting an estimate from a Pro as to what needs to be done. I'd try to find a Pro that kinda 'specializes' in this type of work post-flood. Once you have that, you can see if the Landlord will pick up the entire cost or if you can split it. Thing is, as to why I'm not optimistic, is that your Landlord has already spent some $$$ and he may say to you, "This is it. If the Pro does the work and the problem STILL isn't fixed, I'm not paying any more $$$ for any more work." Then what do you do? If you can move out, I'd do so.
At whatever point you choose, if the home is STILL 'inhabitable', talk to the Tenant Rights Group in your area/County/whatever. Ask the local Municipality. Maybe an Inspector will get involved. DO realize that you want to think ahead of your actions and what they will have on your Landlord. If you p--- him/her off enough, whow knows how he/she will react.
Now, as to why you're still having the problem, maybe a Return Duct is sucking in air from the damp crawlspace. Find them all and see where they lead. Then, see if that 'area' has mold/mildew/dampness, and see if you can 'fix' it. (All my return ducts are in the main house. Crawlspaces are traditionally damp and such. In my home (in which I have one that's 15' x 30', it's always a little damp. I do have a few vents but mold/mildew isn't a problem (and I don't have any 'air' from the crawl being 'sucked into' my HVAC system.) Again, I think the best thing to do in the short term is to have a flood-experienced Pro do a COMPLETE evaluation, and go from there. Unless your Landlord is REALLY heart-warming, I think your chances aren't good. That's just my opinion (from personal experience.)