My configure command:
./configure --prefix=/usr/local --with-apxs=/usr/local/bin/apxs --enable-versioning --enable-track-vars --enable-ftp --enable-xml --with-mysql=/usr --with-pgsql=/usr/local --enable-safe-mode --with-openssl=/usr --enable-bcmath --with-bz2 --enable-sockets --enable-memory-limit --with-jpeg-dir=/usr/lib --with-xpm-dir=/usr/X11R6/lib --with-ttf=/usr/X11R6 --with-gd=/usr/local/gd --enable-gd-imgstrttf --enable-gd-native-ttf --with-mhash=/usr/local --with-mcrypt --with-t1lib=/usr/local --with-gettext --enable-freetype-4bit-antialias-hack


The configure part of GD:
checking whether to enable truetype string function in gd... yes
checking for libjpeg (needed by gd-1.8+)... yes
checking for jpeg_read_header in -ljpeg... yes
checking for libXpm (needed by gd-1.8+)... yes
checking for XpmFreeXpmImage in -lXpm... no
no
checking whether to include GD support... yes (static)
checking for gdImageString16 in -lgd... no
checking for gdImagePaletteCopy in -lgd... no
checking for gdImageColorClosestHWB in -lgd... no
checking for compress in -lz... no
checking for png_info_init in -lpng... no
checking for gdImageColorResolve in -lgd... no
checking for gdImageCreateFromPng in -lgd... no
checking for gdImageCreateFromGif in -lgd... no
checking for gdImageWBMP in -lgd... no
checking for gdImageCreateFromJpeg in -lgd... no
checking for gdImageCreateFromXpm in -lgd... no
checking whether to include FreeType 1.x support... yes
checking for T1lib support... yes
checking for T1_GetExtend in -lt1... yes
checking whether to include GNU gettext support... yes


The error when compiling:
/bin/sh /tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/libtool --silent --mode=link gcc  -I. -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/ -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/main -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1 -I/usr/local/apache/include -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/Zend -I/usr/X11R6/include/freetype -I/usr/local/include -I/usr/local/gd -I/usr/include/mysql -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/ext/xml/expat/xmltok -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/ext/xml/expat/xmlparse -I/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/TSRM  -DLINUX=2 -DTARGET="httpsd" -DUSE_HSREGEX -DUSE_EXPAT -DAPACHE_SSL -DXML_BYTE_ORDER=12 -g -O2   -o libphp4.la -rpath /tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/libs -export-symbols /tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/sapi/apache/php.sym -avoid-version -L/usr/lib/lib -L/usr/X11R6/lib/lib -L/usr/local/gd -L/usr/X11R6/lib -L/usr/local/lib -L/usr/lib/mysql  -R /usr/lib/lib -R /usr/X11R6/lib/lib -R /usr/local/gd -R /usr/X11R6/lib -R /usr/local/lib -R /usr/lib/mysql stub.lo  Zend/libZend.la sapi/apache/libsapi.la main/libmain.la regex/libregex.la ext/bcmath/libbcmath.la ext/bz2/libbz2.la ext/ftp/libftp.la ext/gd/libgd.la ext/gettext/libgettext.la ext/mcrypt/libmcrypt.la ext/mhash/libmhash.la ext/mysql/libmysql.la ext/openssl/libopenssl.la ext/pcre/libpcre.la ext/pgsql/libpgsql.la ext/posix/libposix.la ext/session/libsession.la ext/sockets/libsockets.la ext/standard/libstandard.la ext/xml/libxml.la TSRM/libtsrm.la -ldl -lpq -lmysqlclient -lmhash -lmcrypt -lltdl -lt1 -lttf -lgd -lX11 -lXpm -ljpeg -lbz2 -lcrypto -lssl -lresolv -lm -ldl -lcrypt -lnsl -lresolv -L/usr/lib/lib -ljpeg -L/usr/X11R6/lib/lib -lXpm -L/usr/X11R6/lib/lib -lX11 -L/usr/local/lib -lt1
/usr/local/gd/libgd.a(gd.o): In function `gdImageColorResolve':
gd.o(.text+0x69c): multiple definition of `gdImageColorResolve'
ext/gd/.libs/libgd.al(gd.lo):/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1/ext/gd/gd.c:322: first defined here
/usr/i386-slackware-linux/bin/ld: Warning: size of symbol `gdImageColorResolve' changed from 243 to 226 in gd.o
collect2: ld returned 1 exit status
make[1]: *** [libphp4.la] Error 1
make[1]: Leaving directory `/tmp/build-php-4.0.4pl1-i586-1/php-4.0.4pl1'
make: *** [all-recursive] Error 1


Notes:
I don't have any other versions of gd installed, this is a fresh install. I've tryed in it in 2 different computers, and get the same error. GD version installed is 1.8.4.