Hello,
We have done a lot of tests and the results are in this post:
http://www.phpdocx.com/blog-news/phpdocx-35-general-performance-benchmark
I mean that maybe there're something on your server that could be optimized. Because the tests we have done on three servers (Debian, Ubuntu and Windows) show that PHPDocX is very fast.
Of course you could send us the script you're using (and the template) to run it and see how long it takes.
Regards