This is probably not too hard for me to get fixed up - I can see other users running into this issue down the road as well. I'll try to get it into the next core update.
The daily backup runs as a "shutdown process" from the event queue, which also can process other items (such as a conversion) - I don't think this is actually related, it just happened to cause an error during that queue process which was kicked off by daily maintenance.
If you're at media dir 15, then that is 15,000+ profiles - it likely could still be trying to complete.
Yeah you cannot use multi line CSS comments like that - each comment line needs to be proceeded by // only.
The only way to prevent JR from merging and handling the CSS is to turn on developer mode in the Developer Tools module (not recommended) or simply just modify your meta.tpl file in your skin directory and put in your own URLs to your own CSS files.