Ok, so i tried to do manually what my compilation script does (i'm updating my coompilation script from FT2.4.6 to 2.4.12):
./configure
make
And it worked.
Looking at the compile arguments difference, i notice that i have an additional -I brought by CFLAGS that points to a directory of includes to other libraries i build myself. Removing that includes path makes my automated build work too.
But the only library i see in that path that could impact freetype is zlib (1.2.5 in my own include path, 1.2.3 found by default on the system). Does freetype depend on a specific version of zlib or some other library? I'm using centos 5 32bit with gcc 4.1