Java applets don't work at all (not detected by browser) if IE is launched normally. I'm currently using the latest version of Java 7u60 with Internet Explorer 11 on Windows 8.1. This issue seemed to have popped up randomly as the websites I've been using have just stopped running the Java app. Finally, it works fine in Chrome.
Have already tried reinstalling as administrator with both older version, but the issue still occurs.
Edit: A fresh reinstall of Java 7u67 did not fix the issue.