Upfront and Scribe not committing changes except for text

I'm new to Upfront and WPMUDEV. I have installed Upfront and Scribe on a new multi-site install. I'm making changes in Upfront and everything seems to save, but only the text changes appear to be committing. I've tried to set a global header, but that doesn't take either. I'm sure I'm doing something silly. TIA!