I'm having the same problem on a Sun Cobalt RaQ installing  PHP 4.0.6 and libgd 1.8.4 and libpng 1.2.0

Running ldconfig -v shows me: (excerpt)
/usr/lib:
        libpng.so.3 => libpng.so.3.1.2.0
        libgds.so.0.orig => libgds.so.0.orig
        libgd.so.1 => libgd.so.1.2
/usr/local/lib:
        libpng.so.3 => libpng.so.3.1.2.0
/usr/local/src/libpng/libpng-1.2.0:
        libpng.so.3 => libpng.so.3.1.2.0
/usr/lib:
        libpng.so.3 => libpng.so.3.1.2.0
        libgds.so.0.orig => libgds.so.0.orig

So libpng seems to be installed properly. But no ImageCreateFromPng!

Running phpinfo(); shows me:
gd
GD Support enabled 
GD Version 1.6.2 or higher 
FreeType Support enabled 
FreeType Linkage with TTF library 
WBMP Support enabled 

I have tried in the php_config.h to insert the line 
#define HAVE_GD_PNG 1 

and my command line is:

./configure --prefix=/usr --with-regex=system --enable-calendar --with-db --without-dom --enable-filepro --with-gettext --enable-sysvsem --enable-sysvshm --enable-track-vars --enable-trans-sid --disable-debug --with-imap=shared --enable-ftp --with-gd --with-apxs --with-zlib --with-pcregex=/usr --enable-sockets --enable-freetype-4bit-antialias-hack --with-xml=shared,/usr --with-yp --with-mysql=shared,/usr/local/src/mysql/mysql-3.23.40-pc-linux-gnu-i686/mysql-3.23.40/ --with-ttf --with-apxs --with-zlib --with-png-dir=/usr/local

Any ideas?