I've upgraded my site (to 1.4.1) into a temporary directory in my current site. I've copied over my only theme (Professional, I think slightly modified) without any changes into my layouts folder. The colors and everything are correct, but the text size is different, the spacing is off, and my copyright message at the bottom is back to being the default.
The text size and spacing I would think would be controlled by the style.css file in my theme, but the two files are identical.
Original site
Upgraded site
I know, I know, read the manual, but everything seems to suggest that the style is controlled by the theme, and the two theme folders are identical.