I'm not sure if this is an issue with both site clients; or even on some other platform like, Armor Games I think? But basically I got this message:
SecurityException
Missing required Permissions manifest attribute in main jar:
http://download.threerings.net/spiral/client/getdown-pro.jar
This happened after I updated my Java to 7 update 51, where I accidentally clicked something about the security prompts.
I'm not sure if this just affects Kongregate or both the Site client as well. As for this account I usually play with the downloaded client so I have no issues.
I had this problem too, playing on Kong, running fine 'til this last Java update.
I'm not that great with advanced options, but browsing through Java tutorials and guides, I found out there's this option to configure it.
When you're there, go in security tab and add both
http://download.threerings.net
http://www.spiralknights.com
to exceptions list.
It should run fine, at least it worked for me, after doing so.
Configure Java -> Security -> Edit Site List -> Add -> *add those two sites* -> OK -> Continue
I added www.kongregate.com too to be sure, but I don't think it affects the whole thing in any way.
Hope this works, have fun!