WPMUDEV not working with Sydney Theme

I've gotten with my hosting over the past 3 days since I installed WPMUDEV. It is a great concept and idea, but for some reason it keeps taking down my website. I had godaddy do a bunch of research on it and they could be wrong but they are pinpointing that plugin as the problem. Let me know if it get's fixed as I have over 500 domains and lots more development work to do. I appreciate it.