I was recently upgrading a Thesis-based site from Thesis 1.8 to 1.8.4 and noticed that every time I activated the theme, the site’s style was completely wrong. I checked the HTML generated by both versions, and 1.8 was requesting the Thesis style.css but 1.8.4 was not. Upon looking at the code, I found that in 1.8.4 when the design options are saved, Thesis copies the contents of style.css to custom/layout.css.
Solution: Once you have activated Thesis 1.8.4, simply go to the design options panel and click the big ass save button. This will run the Thesis code that copies the style.css rules into custom/layout.css – your design should now look as before.