If you find your Suffusion theme custom CSS stops working then this post may help.
We recently updated a website using Suffusion 4.4.7 to WordPress to 4.3.1 from 4.1.8. After doing this there was a problem with the display of the website in particluar the NextGEN plugin photo galleries which are heavily customised.
We were using the Suffusion theme Custom Includes facility to apply our custom CSS but it seemed some (maybe all) of it was being ignored after the upgrade. Using the Firefox browser add-in Firebug to check the CSS on the fly against the website showed the custom CSS we had was still correct but it was being ignored or not applied. Clearing cache etc didn’t fix the problem.
On several other websites we look after we use the Simple Custom CSS plugin to add our own styles to override the default CSS of a plugin or theme. So, given we were in a hurry, as a test, we simply installed the Simple Custom CSS plugin and then cut/pasted the custom CSS from Suffusion into the Simple Custom CSS plugin. Refreshing the browser page/s showed that the dislay of the website was back to normal.
What the root cause of the problem was we don’t know. We like Suffusion but as we’re planning to move that website off the Suffusion theme to another one (to implement WooCommerce) we weren’t inclined to spend much time looking into the problem and so went for a quick fix.