Hi Thruna/Stefan
Apologies for the short delay in response as I am only seeing this updated posting now 
Now regarding the scenario Thruna mentioned: replacing "Get Support" link in CerLogonPage.jsp and logonPage.jsp and added a new branding image file and subsequently deployed the EAR file.
- Then you changed the UME properties (image, alias) Restarted the portal server.
- You can only seem the branding image in the http://<host>:<port>/nwa/auth logon page.
- You can't see any image in http://<host>:<port>/irj/portal logon page
As you mentioned there is the possibility that this could be deployment related. Now in order to check this and proceed with analysis you can check the deployment by navigating to :
\usr\sap\<sid>\<instance-id>\j2ee\cluster\server0\apps\sap.com\irj\servlet_jsp\irj\root\WEB-INF\deployment,\pcd ,\tempand \pcdContent
- If you find any files with .err extension there, kindly remove the .err extension.
- Then restart the J2EE engine.
Should the issue still not be resolved and there does not exist any.err files,kindly locate following * files in the deployment directory and remove the * extension and restart the J2EE engine.
com.sap.portal.design.dataprovider.par.bak
com.sap.portal.design.portaldesigndata.par.bak
com.sap.portal.design.themepartregistration.par.bak
com.sap.portal.design.urdesigndata.par.bak
Note: Please make sure that you do not delete the entire file,you onlyneed to remove the .err or * extension.
Lastly after performing the checks outlined above kindly proceed and check the PCD inconsistencies as per note number 1086644.
Kindly update me as per your findings.
Kind Regards
Troy Cronin - Enterprise Portal Support Engineer