actually I found the problem. In the utilities folder there is a program called "Java Preferences" and Java needs to be activated in there now as well as in browsers. I guess that must be an issue with the new Java update.
But does anyone know if this is normal:
0 drwxrwxr-x+ 48 root admin 1632 Apr 16 13:48 .
0 drwxr-xr-x 32 root wheel 1156 Apr 24 09:24 ..
32 -rw-rw-r--@ 1 root admin 15364 Apr 27 13:21 .DS_Store
0 -rw-r--r-- 1 root wheel 0 Jun 13 2011 .localized
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Address Book.app
0 drwxr-xr-x@ 4 501 staff 136 Apr 11 15:24 Adium.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 App Store.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 Automator.app
0 drwxr-xr-x@ 3 501 admin 102 Jul 21 2010 BlueMac.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 Calculator.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 Chess.app
0 drwxrwxr-x 6 root admin 204 Apr 10 16:41 Cisco
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 DVD Player.app
0 drwxr-xr-x 3 root wheel 102 Jul 11 2011 Dashboard.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Dictionary.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 FaceTime.app
0 drwxrwxr-x 7 root admin 238 Apr 10 16:37 Flip4Mac
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 Font Book.app
0 drwxr-xr-x 3 root wheel 102 Jul 11 2011 GarageBand.app
0 drwxrwxr-x@ 3 501 admin 102 Apr 18 14:19 Google Chrome.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Image Capture.app
0 drwxr-xr-x 3 root wheel 102 Jul 11 2011 Launchpad.app
0 drwxr-xr-x 4 root admin 136 Apr 11 13:38 Lotus Application Support
0 d---r-xr-x+ 18 kdpeters admin 612 Apr 11 15:12 MATLAB_R2012a.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Mail.app
8 lrwxr-xr-x 1 root admin 92 Apr 10 16:37 Microsoft Silverlight -> /Library/Internet Plug-Ins/Silverlight.plugin/Contents/Resources/Silverlight Preferences.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 Mission Control.app
0 drwxrwxr-x 4 root admin 136 Apr 11 13:38 Notes.app
0 drwxr-xr-x 3 501 staff 102 Feb 9 2010 Notify.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Photo Booth.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Preview.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 QuickTime Player.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 09:41 Safari.app
0 drwxr-xr-x 3 501 staff 102 Aug 9 2011 Sametime.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Stickies.app
0 drwxrwxrwx 3 35244 admin 102 Apr 10 16:48 Symphony.app
0 drwxrwxr-x+ 3 root wheel 102 Apr 11 08:57 System Preferences.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 08:57 TextEdit.app
0 drwxrwxr-x 3 root wheel 102 Apr 11 14:47 TextWrangler.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 Time Machine.app
0 drwxr-xr-x+ 26 root admin 884 Jul 11 2011 Utilities
0 drwxr-xr-x 3 501 admin 102 Mar 18 12:25 VLC.app
0 drwxr-xr-x 3 root wheel 102 Apr 11 17:20 Xcode.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 iCal.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 iChat.app
0 drwxr-xr-x 3 root wheel 102 Jul 11 2011 iMovie.app
0 drwxr-xr-x 3 root wheel 102 Jul 11 2011 iPhoto.app
0 drwxr-xr-x+ 3 root wheel 102 Apr 11 08:57 iTunes.app
should everything really be owned by root? I'm wondering if that was messed up by my following the instructions to change the short user name