CSS disappears

First of all, this is a great plugin. Especially to kickstart a new WordPress site.
However I noticed that one of my CSS items started to disappear. Just out of the blue, one day all is great, the next day, without any (to my knowledge) changes one of the CSS items was no longer embedded in the body.
When I changed it to external file it started working again. Than a few days later it disappeared again. Needing a re-save, or change to include in the body instead of an external file.
I do have a caching plugin, which was not active at the moment (wp super cache).

Anyway, I suppose this might well be a fluke, owing to my specific configuration, or the forums would probably be awash with similar topics.

I decided to move my CSS and JS to a custom plugin where I can do the minification, concatenation, obfuscation etc in a build script and use git to push / pull to production. So unfortunately I cannot do any testing / debugging. I just wanted to let others know. If more people experience the same issue, something somewhere might be wrong ??

Thanks again for this amazing plugin!