Portal problem in navigation after upgrade Service Pack 25 (SP25)

Hi experts,
We have upgraded our NetWeaver 2004 (6.40) environment with Portal 6.0 to the latest Service Pack 25 (SP25).
After the whole upgrade a strange problem occurs in the Portal when using the portal navigation. After a few clicks in the navigation a JavaScript error in the browser occurs. We use Internet Explorer 7 and 8.
When the error occurs, we have to refresh the browser to use the portal again. I have the idea that the problem is relating to the session management but i can't figure it out.
Any ideas?
JavaScript error details:
User Agent: Mozilla/4.0 (compatible; MSIE 8.0; Windows NT 5.2; Trident/4.0; GTB6; .NET CLR 1.1.4322; .NET CLR 2.0.50727; .NET CLR 3.0.04506.30; .NET CLR 3.0.04506.648; .NET CLR 3.0.4506.2152; .NET CLR 3.5.30729)
Timestamp: Mon, 25 Jan 2010 11:29:53 UTC
Message: Permission denied
Line: 944
Char: 39
Code: 0
URI: http://portal.url.com:50000/irj/portalapps/com.sap.portal.epcf.loader/script/standard/js13_epcf.js?6.0810
Edited by: J. Weghorst on Jan 29, 2010 11:11 AM

Dear Benjamin,
Thank you for your answer. I think it helped us with the scope of the problem.
We use a FQDN for the Portal and also a FQDN for the backend (R/3). There is nothing changed in those hostnames between the upgrade from SP19 to SP25. The browser problem occurs after a few clicks (10 - 30) in the left-side navigation and is not based on time or specific iView. So its difficult to find a routine structure in the presents of the error.
I have also used the tool to analyse the JavaScript code. It gives a error on a not defined object value within the file js13_epcf.js?6.0810.
It seems that the part of the code had to do something with the iFrame usage of the Portal. But it's to difficult to find the real cause of the issue.
Any ideas? Thanks in advance.
Edited by: J. Weghorst on Feb 1, 2010 4:51 PM

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