If I understand you, you used configure/make/make install to install version 0.9.60. Unless you told it not to, that process installs wine into /usr/local. It appears you also have a version of wine installed in /usr, probably 0.9.56. That probably means you have installed a binary package of wine using your distribution's package manager. You should uninstall wine using the package manager; once you've done that, the version you installed with configure/make/make install should work fine.
