We had been using the Cloner plugin to clone sites for several weeks with no issues. After the last update, the cloning process is not working correctly.
Here is the site we cloned: http://test-hopewell.roundrockisd.org/
This is the site that we cloned to: http://test-cdfulkes.roundrockisd.org/
In the theme options, there is a place set Accent Color, which determines hyperlink color, and several other elements on the page, including the navigation bar font colors.
Before the update, we would just change the color after the clone process, to the new school's colors, and everything changed. Now, changing that accent color has no effect. The colors on the CDFulkes site show as green (like the Hopewell site), even though the color is set to maroon.
From our research, it looks like the sites are pointing to the same CSS style sheet. On previous clones, it created separate folders and stylesheets for each site.