Okay, I tested a few times in RC4 and was able to replicate up until I edited custom.css when editing CSS in Themes. I did notice the CSS/JS was gone from all the hooks I'd installed. This was prior to doing anything but upgrading to RC4 so I think it may be an IPS bug. I'll submit a bug report to see. Is the CSS at least appearing under /core/front/custom in Appearance > Themes > Edit HTML and CSS > CSS? I was able to get the CSS to be compiled on the frontend by editing custom.css under the same sub-folder in the Themes editor and then emptying the IPS cache folder . I didn't test in Designer's Mode, just the Themes web editing.