The usage of AC_ARG_ENABLE is roughly:

  AC_ARG_ENABLE(name, help, if-provided, if-not-provided)

i.e. the third argument gets executed if either --enable-foo or --disable-foo is passed, and the fourth if neither.

The new code states:

    AC_ARG_ENABLE([pathchecks], [AC_HELP_STRING([--enable-pathchecks], [Enable checks for paths, access and execution @<:@default=yes@:>@])],
    [
        NETCAT_RUN=skip
    ], [
        AC_MSG_CHECKING([for hddtemp being queryable via netcat])
        NETCAT_RUN=([`"$NETCAT_PATH" "$NETCAT_HOST" "$HDDTEMP_PORT" 2> /dev/null`])
        AC_MSG_RESULT([$NETCAT_RUN])
    ])

i.e. the checks will be skipped both with --enable-pathchecks and --disable-pathchecks, and run only if neither is passed. I don't think that's what you wanted.