I would recommend checking to see if you have sip installed in different locations, with the newer version being in a path that is not at the head of your PATH
.
mdfind -name sip | grep '/bin/'
This should tell you all of the sip binaries on your computer. Check the version of all of them, and then make sure that path is at the front of PATH
What it could actually be, regardless of it seeming like you only have one sip, is a leftover .pyc
file that is getting picked up before your intended sip. Try this to confirm:
$ python
>>> import sipconfig
>>> print sipconfig
This will tell you where it is finding sipconfig. If it looks like the wrong spot, or if you check it and all that is left is the pyc
file, remove it. Then your newer sip should be found properly.