OK, So I went to the last application back-up of 30 August 2013. And replaced the new broken version with that older version. Then I turned off my internet so it couldn't update. Started it. Turn off update. Then turned on my internet.

So far it seems to be working

It says "1229 updates are available"

Also if I go to About JDownloader it says "-last09- Version 0.9.581"

So the new version that doesn't work is the same version number of an older version that does?

While that doesn't make much sense. Either whatever was broken yesterday should be fixed in a new update, or the previous version should be put up for download.