My configure line:
./configure  \
--with-gd --with-oracle=/u/oracle7 \
--with-mysql \
--with-config-file-path=/h/home/www/conf \
--with-apxs=/h/home/www/bin/apxs \
--enable-debug --enable-magic-quotes=yes \
--enable-memory-limit=yes --enable-url-fopen-wrapper=no \
--enable-sysvsem=yes --enable-sysvshm=yes  \
--enable-track-vars=yes --with-system-regex \
--enable-versioning --enable-safe-mode

I faced the problem when HTTP_*_VARS were no set. I dig it out and found that sometimes gpc_order 
variable in php3_ini structure contains garbag like "mod_php3.c" or "<IfModule>". 
Later I found that in function 
static void *php3_merge_dir(pool *p, void *basev, void *addv)
I get this garbage from basev.

So I looked at *php3_create_dir(pool * p, char *dummy)
function to find out what is wrong.
I changed code of this function to make it more understanable and (IMHO)
more correct.
So, here is my version of this function (all stuff related to mod_php3.c):
/*
 * Create the per-directory config structure with defaults from php3_ini_master
 */
static void *php3_create_dir(pool * p, char *dummy)
{
    php3_ini_structure *new;
    static int first_time = 1;

    php3_module_startup();
    new = (php3_ini_structure *) palloc(p, sizeof(php3_ini_structure));

    memcpy(new,&php3_ini_master,sizeof(php3_ini_structure));

    return new;
}