Perhaps the issue here is that you are installing a local version of Python with the same configured prefix as a system installed Python of the same major version.  This is a primary use of the --prefix option to the ./configure script of Python.  You should ensure that each Python x.y instance is built and installed with unique values for --prefix; that should ensure that there is no conflict among those instances with regard to their "global" file paths.  That said, there can still be conflicts with --user locations where the same user-specific paths are used by all instances of a particular Python major version.