I had created my own templates and minimal changes to the css, all working well. When I upgraded to 1.9.1, all the styles for the journal are gone? I can see the styles in the journal when I look at the default theme _active but when I use my theme, the styles are not there? did the upgrade change the links to CSS files?

The new version should not have changed any of the css files. What was the exact path for the css file that you made changes to, before upgrading?