Davey Shafik has a recent post to his blog about what he calls "The Blowfish Debacle" - the issues that came up with the PHP 5.3.7 release to upgrade the crypt_blowfish version that resulted in a larger error being introduced.
This was a great security fix, solving an issue with insecure passwords due to incorrect behavior. HOWEVER, what wasn't made clear, is that this change was actually a backwards compatibility break. If you upgraded to 5.3.7+ data hashed pre-5.3.7 would no longer match data hashed post-5.3.7; this means if you use it for passwords, it will no longer match. So what's the deal here?
He talks about the differences in the two methods of encryption, the newer being the "more correct" way of doing things. If you need the backwards compatibility because of previously hashed values, you can use the "$2x$" prefix instead of the usual "$2a$". He includes a snippet of code that can be used to upgrade all of your previously hashed blowfish passwords up to the new format.