Glad to hear he checked out and there is nothing to worry about
One time I crated Missy for about 2 hours while I stepped out when I came home her face smelled sooo bad! I thought something was wrong I couldnt imagine how she got so stinky in just 2 hours, I finally figured it out, she some how released her anal glands and cleaned herself up
so gross!
The smell washed away with a good bath and hasnt happened since, maybe that happend to your little guy. Give him a wash and see if it comes back again. If it does it must be the breath and eye goobers LOL