It's hard to say what the cause of the odor is, or where it's coming from. If you've done all that you can to eliminate the odor, such as cleaning the walls and floors with a mold/mildew mixture, then the source of the problem has to be "where you can't see it".
If the smell is actually urine-type or bowel-type, you could have a 'gas leak'. Perhaps the smell is emitting from the waste pipe, and 'leaking' out from under the toilet. You can only check this by removing the toilet (which involves a few things when replacing it.) If you're not familiar w/removing and replacing the toilet, just buy yourself a good book about Plumbing. It's WELL worth it. Reader's Digest and Time/Life publish such books, among others. Even the Home Centers have books. Just ask the Guys in the aisles for the 'specific' repair book.
My best to ya and hope this helps.
Jay J -Moderator
PS: You may end up having to rip up the flooring. If that's what it takes to remove the smell, then that's what it takes ...