I came in here because I added W3 Total Cache to my Graphene-based site. It obliterated the formatting.
After reading a few related threads in here, I believe I fixed my problem.
1) With W3 Total Cache activated, go to “Performance” in the left dashboard menu.
2) Under “General Settings” find “Minify.”
3) Disable that.
Minifying code is a great way to speed up page load, but it is not essential, and, for me, that is where the two were in conflict.
This is obviously resolved for me, but hopefully this will help someone else, too.