I believe this problem was discovered in January of this year when I was trying to integrate the ASP.NET menu into DNN.  Here is the note on a change I checked in.

Minor fix to prevent the container ID from getting a dash in its name.  This will happen when the ModuleID = -1 since it gets appended to the id.  The module ID is -1 when its an admin container.  The dash became a noticeable issue when trying to work with the ASP.NET 2.0 Menu.

So it looks like it will be fixed with the next release.  In the meantime, if you wish to try out the fix to make sure it covers your issue, open up the Admin\Skins\Skin.vb file and locate this line

' make the container id unique for the page
If Not objPortalModuleBase Is Nothing Then 
 ctlContainer.ID += objPortalModuleBase.ModuleId.ToString
End If

Change it to

' make the container id unique for the page
If Not objPortalModuleBase Is Nothing AndAlso objPortalModuleBase.ModuleId > -1 Then 'Can't have ID with a - (dash) in it, should only be for admin modules, where they are the only container, so don't need unique name
 ctlContainer.ID += objPortalModuleBase.ModuleId.ToString
End If