Why are you doing it manually? I used the Open XML SDK and it worked smoothly.
You have basically access to the whole xml tree so you can change almost anything you want, with the exception that the library takes care of zipping and unzipping.
The SDK has also a viewer where you can have a better look at the file, and what I've found is that most docx documents have internally multiple files zipped together. Maybe you are missing one of them.