We have since had a chance to look into this issue further and discovered that these warnings have started to occur due to a conflict between the new security approach Oracle presented in Java 7 Update 21 and the current version of the Java based uploader that is available on our site.
The combination of signed and unsigned code which is being labeled as “potentially unsafe” by Java is part of the third party uploader we are using so we cannot address this issue on our own, but we have reached out to the developer of the uploader for further assistance.
For the time being, you can potentially prevent these warnings from being generated when you upload from Firefox or Chrome disabling the Mixed code security verification seeing that is enabled within Java 7 Update 21 by default.
If you would like to do this, you will first need to open your Java Control Panel using the instructions on the following page of the Java website: http://www.java.com/en/download/help/javaconsole.xml
From within your Java Control Panel, you can disable this setting by clicking the “Advanced” tab, checking the radio button next to “Disable verification (not recommended)” in the section called “Mixed code (sandboxed vs. trusted) security verification” and then clicking the “OK” button.
I hope this helps.