Our python is installed on a shared directory that is accessed through a symbolic link. 
$ which python3.4-config
/Produits/publics/x86_64.Linux.RH6/python/3.4.1/bin/python3.4-config

$ ls -al /Produits
lrwxrwxrwx 1 root root 13 Oct 31  2013 /Produits -> /nfs/Produits

With this configuration python-config returns a wrong path (it gives a double /nfs prefix)

$ python3.4-config --includes
-I/nfs/nfs/Produits/publics/x86_64.Linux.RH6/python/3.4.1/include/python3.4m -I/nfs/nfs/Produits/publics/x86_64.Linux.RH6/python/3.4.1/include/python3.4m


The problem is due to a double string replacement in the script

   prefix_build="/Produits/publics/x86_64.Linux.RH6/python/3.4.1"
   prefix_real=$(installed_prefix "$0")

   # Use sed to fix paths from their built-to locations to their installed-to
   # locations.
   prefix=$(echo "$prefix_build" | sed "s#$prefix_build#$prefix_real#")
   exec_prefix_build="${prefix}"
   exec_prefix=$(echo "$exec_prefix_build" | sed "s#$exec_prefix_build#$prefix_real#")
   includedir=$(echo "${prefix}/include" | sed "s#$prefix_build#$prefix_real#")

for $includedir the replacement of $prefix_build by $prefix_real is applyed twice and since the $prefix_real contains $prefix_build it produce a wrong result.

In addition I think it is strange to have lines like the following
prefix=$(echo "$prefix_build" | sed "s#$prefix_build#$prefix_real#")

Do you want to provide a patch?

I stumbled across the exact same problem and I have made a fix that is working, at least for the usage I have...

I don't understand: Why python-config needs to seek "realpath"? Why python-config is trying to be smarter than one who starts ./configure script?

As so, the right thing to this, is remove "smart" parts from python-config. But as for fast hack in to this is replace line 'prefix_real=$(installed_prefix "$0")' with 'prefix_real=$prefix_build'.

I've submitted a pull request with another fix. I've tried to keep the changes at minimal but I couldn't stand keeping meaningless 'echo $x | sed -e s/$x/$y/' ;-).

I have to point out that the attached patch is wrong since it does readlink on CFLAGS &c.

New changeset 14086cfc5eed8c5e78342d79e5db87a135d75fa8 by Benjamin Peterson (Michał Górny) in branch 'master':
closes bpo-22140: Prevent double substitution of prefix in python-config.sh (#3769)
https://github.com/python/cpython/commit/14086cfc5eed8c5e78342d79e5db87a135d75fa8

New changeset 68b131d5b674549bb637b366730497714ad11328 by Benjamin Peterson in branch '3.6':
[3.6] closes bpo-22140: Prevent double substitution of prefix in python-config.sh (GH-3769) (#3793)
https://github.com/python/cpython/commit/68b131d5b674549bb637b366730497714ad11328