Are you using your own SMTP server or sending through the Quickfile server as yourname@quickfile.co.uk?
There is no 100% foolproof way of keeping invoices out of junk folders, the very fact that the email contains an embedded link is sometimes a trigger. However using your own SMTP server is usually the most reliable.
An update in one of the major filtering algorithms can hit many of your customers at the same time so a small change can have a major effect…
Instructions on using your own server can be found in th knowledgebase