Had the same problem. For me, in the end, it turned out to be (probably) something to do with having messed with my apache virtual hosts, and the SSL certificate for the server (I tidied up a few of my virtual hosts and replaced my snakeoil certificate with a genuine one - the latter I suspect was the real cause of my problem).
Solution: What worked for me was to clear out any saved passwords in the clients (I was using Eclipse - subclipse or subversive, I forget which - and Tortoise). I guess that some sort of hashing based on the SSL certificate was being used somewhere along the line to encrypt the saved password, which rendered them inaccessible or invalid when I replaced the certificate.