After SharePoint 2010 MOSS SP2 was applied problem with library preview

Hi,
I have recently applied SharePoint 2010 MOSS SP2 from here
http://support.microsoft.com/kb/2687453/en-us
After I have installed that service pack, one of my custom made library workflow for a department would not work when they Upload a document. It works if they create new documents from library menu, but not if they Upload a new documents.
ULS Viewer gives following messages
MetadataNavigationContext Page_InitComplete: No XsltListViewWebPart was found on this page[/_layouts/Upload.aspx?List=%.......Hiding key filters and downgrading tree functionality to legacy ListViewWebPart(v3) level for this list.
MetadataNavigationContext Page_InitComplete: No XsltListViewWebPart was found on this page[/_layouts/UploadEx.aspx?List=%...... Hiding key filters and downgrading tree functionality to legacy ListViewWebPart(v3) level for this list.
Some but not all taxonomy values were found, this can lead to the catch all being incorrect. Use TaxonomyField.SetFieldValue to update taxonomy values.
Also, when I try to use Navigation in Site Settings, and if I want to add new navigation either link or folder, and if I use IE 8 or 9 (32 bit) in the pop up window Navigation Link - web dialog, there is no "OK" button.
Thank you 

Hi Eric
Thank you for helping me.
I have already came accross this blog and it is now quite the same as my case.
My navigation works without problem.
Also, when I open the site in SP Designer, all views of my library show this library in XsltListViewWebPart.
But this Upload.aspx, is a Form, not a view, and it shows the list in ListFormWebPart.
Just to remind you, the workflow work fine if the use "New Document" menu from library ribbon. So, I assume something is wrong with Update form.
This other form UploadEx.aspx, I do not see in SharePoint Designer for this Library.
I am kind of suspicious that it maybe has something to do with
http://support.microsoft.com/kb/2872441/en-us
And am thinking of applying these
Thank you
Windows Server 2008 R2 for x64-based Systems Service Pack 1
Microsoft .NET Framework 4<sup>[1]</sup>
(2835393)
Remote Code Execution
Critical
2572078 in MS11-078
Windows Server 2008 R2 for x64-based Systems Service Pack 1
Microsoft .NET Framework 4<sup>[1]</sup>
(2840628)
Elevation of Privilege
Important
2656405 in MS12-034

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