Hello again phuynh,
I haven't heard of any conflicts, outside of other robots.txt plugins. It is possible that a sitemap plugin could be conflicting. I have tested most of the major sitemap plugins though. You could of course go through and disable plugins to see if a conflict is happening...again though, I haven't heard of any such conflicts, but anything is possible.
When you publish to network, are any sites updating? How about when you change to a Website from the drop down and update the site directly? When you save your default robots.txt file, does that work correctly?
Also, try this... Network Admin > Sites > Edit a mapped site > Click the settings tab. Then in your browser do a find for the word "robots" and see if any other robots.txt files have been set and not removed by another plugin. You should only see: MS Robots.txt - However, if some other plugin named the setting incorrectly (like is_robots) or some name WordPress typically uses, that may create a conflict.
Outside of this, my attempts to debug via a support ticket is a bit limited. If you would like me to onsite the issue, I would need access to your WordPress install. Which I'm more than willing to do, but can understand why you wouldn't want this.