Hi.
Are you doing it by adding something like the following in source mode?
<style>
* {
background-color: #ff6600;
}
</style>
I was able to reproduce the issue you are describing by including the above, flipping to Visual mode and then saving (tinyMCE removes the <style> tag and comments out the css code).
I entered a ticket on this issue at
https://www.labkey.org/issues/home/Developer/issues/details.view?issueId=11333
There is nothing you can do in the UI to make this work as far as I can tell.
I did find a potential fix for this as discussed in the ticket, but we need to see if there are any undesired side effects before applying it.
thanks!