If you set up the Vacation reply for your Gmail account, there's a few things you should keep in mind.
Make sure you don't add the automated reply in Plain text mode. If you do so, it will break the formatting for the rest of the email including the signature.
If you have previously used the Plain text option and change it now, you need to save your progress. Due to a known bug, you might not be able to Save the changes at the bottom of the page. An easy workaround is to edit the response slightly (e.g. adding a SPACE to it.) This should activate the "Save" button again.