Unfortunately I can’t post the site yet (company rules — but thanks!), but I looked into the problem and it looks like it is a theme specific problem. The original theme css is loaded first, followed by some javascript and then followed by the new custom css. This may cuase the old theme to be visible for a brief moment while the javascript is executing and the browser has not yet had a chance to get to the new css.
I got around this problem by directly modifying the original theme css. Not an ideal solution but it works for now.
