Span tags being stripped in TinyMCE in Chrome

I am developing a new site and have run into a very specific bug that is causing quite a few headaches.

We wanted to have some very specific styling on select images, so we added a custom button to TinyMCE that when clicked it would insert a span tag with a particular class around the image. This insertion works perfectly, and we can save the page and it all looks good.

However, when in Chrome if you delete a blank line the span tags will get removed from the post. It is not just the ones from the custom, but any span tag that has been entered. Also, I tried this in another install without my custom button and it also removes the span tags.

Firefox handles this fine and does not remove span tags, so it seems to be a specific Chrome/tinyMCE issue.