I was having a similar problem, and I managed to resolve it. Some JavaScripts on my home page were failing to work. I used Firebug to investigate and saw an error stating that "dnnConfirm is not a function". After some debugging, I found the bug: It seems that some of the new DNN 6 features (ex: the "Manage" button and menu) rely on a new JavaScript library. This library was not being loaded.
The new RIBBONBAR control panel that ships with DNN 6 automatically loads the required JavaScript, so the other administrative functions work correctly as long as you're using that control panel. But if you change to a different control panel, the JavaScript library is likely not being loaded.
I was using a control panel that I built, so I changed my Page_Load to include the following:
DotNetNuke.Framework.jQuery.RequestRegistration();
DotNetNuke.Framework.jQuery.RequestUIRegistration();
DotNetNuke.Framework.jQuery.RequestDnnPluginsRegistration();
These statements will load jQuery, jQuery UI and the DotNetNuke JavaScript libraries, respectively. You should be able to add this code to any control panel. It could be done either in the code-behind (.cs or .vb) or in a server-side script tag in the .ascx source.
The built-in control panels can be found in the /Admin/ControlPanel/. If you are using a third party or custom control, you can find out the source location. Go to Host > SQL and paste the following command:
SELECT [ControlKey], [ControlSrc] FROM {databaseOwner}{objectQualifier}ModuleControls WHERE [ControlKey] like 'CONTROLPANEL%'
This will produce a list of all of the control panels in your DNN installation. Again, all should be editable, and adding the references should resolve the "dnnConfirm is not a function" problem.
BTW, I am running DNN 6.0.2. I have not tested whether the problem has been fixed in 6.1.x, or whether this workaround still solves the problem.