Safe mode appears to be malfunctioning. I've enabled safe mode for the whole server, php scripts appear to work fine, but when a php script attempts to write a file (in a directory owned by the same user as the php script), php complains it can't write.
For example, using imagejpeg to export a jpeg file, results in :
    Warning: imagejpeg: unable to open
    '/home/photo-user/html/pictures/05090027.JPG'
    for writing in /home/photo-user/html/functions.inc.php on
    line 35

Using fopen to write a file gives the same result, so I believe it to be a general permission problem.

Also, when I try to use convert (image conversion utility), located in /usr/local/bin (I have added php_admin_value safe_mode_exec_dir /usr/local/bin/ to the Apache config), I get a shell return value of 154 (can't find what it means). PHP should be able to execute that file and have it converting images (writing them back to the directory owned by the user running the php script).


The full configure :
./configure  --with-apxs=/usr/local/apache/bin/apxs --with-imap --enable-versioning --enable-ftp --with-mysql=/usr/local/mysql --with-snmp=/usr/local/snmp --with-openssl=/usr/local/ssl --enable-dbase --enable-debug --with-pear --with-mcrypt --with-dom --with-pcre --with-zlib-dir=/usr --with-jpeg-dir --with-gd --enable-exif