Correct — after the first try on any subsite, when I click “Save Stylesheet” (with “Add this to the theme’s stylesheet” selected), the CSS that I typed into the box just disappears, and it goes back to the default “Welcome to Custom CSS!” text. After the second try, it saves.
– WP version: 3.5.1
– WordPress.com Custom CSS plugin version: 1.5 (note the plugin name — it’s not SafeCSS, but if I remember rightly that’s the plugin’s former name)
We have Jetpack Lite installed instead of Jetpack, but maybe we’ll upgrade. I’m sure it could also be a plugin conflict, so I could also troubleshoot by turning off all the other plugins on our test site and turning them back on one at a time — perhaps I will; I just never got around to it.