The Apache user has write perms on directory.

script:
if(!$fp = dba_open("test.db", "c", "db3")) {
        print("error");
        exit;
}
dba_insert("testkey", "testval", $fp);
echo( dba_fetch("testkey", $fp));
dba_close($fp);

what is does, is just opening a file "test.db", that has 0 bytes and causing the error 

Warning: driver initialization failed in /path/to/script.php

opening already existant db3 files doesn't work either.

changing the handler from db3 to db2 works fine

configure line: 
./configure --with-apxs=/usr/local/apache/current/bin/apxs --with-mysql=/usr/local/mysql/current --with-zlib --with-ftp --with-jpeg-dir=/usr/local/lib --enable-versioning --enable-track-vars=yes --enable-url-includes --enable-sysvshm=yes --enable-sysvsem=yes --with-config-file-path=/etc --with-db3=/usr/local/BerkeleyDB.3.2 --with-db2=/usr/include/db2 --with-sablot --enable-dbx

i am using sleepycat's BerkeleyDB 3.2.9

hope, that's it