McChain,
the latest Version is not only blocking Java on Websites it is also blocking java-based (eclipse-based) software e.g. RSSOWL.
After having installed the upgrade it is also blocking an long before installed open-vpn based Software (tunXten)
Also adding a footer to all of my latest e-mails like "Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv. " = This E-mail is free of Virus and mailware due to an active avast! antivirus protection" is from my point of view not acceptable.
So I would highly appriciate that you check your software and explain to your customers why something like that happens.