Well, it turned out that my last assumption was correct.
I deleted the wrong content from these pages and installed the File manager, event viewer etc in their appropriate pages and all (Well, who knows :) )  seems to be OK now.

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Yehuda Tiram
AtarimTR

972-2-5700114   |   972-54-4525492   |    http://www.atarimtr.co.il

I did not explain it right, sorry.
I exported 495 portal (pages and content) and imported it to a new install of v544. The import was done during the first install of the new 544.
(I copied the 2 exported template files (.template.resources + .template) from 495 to the “default” dir of the new installation BEFORE I installed the new v544 site. Then selected this site template from the drop down while was asked by the installation wizard.)
What happened (to my understanding) is that the exported template installation overwrite some of the admin tabs MODULES (like file manager and event viewer) since it already had those definitions in the TabModules table (I may be wrong here, it is just a guess but the solution I used worked).
My point of saying that the new admin pages (like taxonomy) did not messed up was that they were not part of v495, hence their definitions could not be overwritten.
That made me lift my eyes to the page title (well, not very clever I did not do it before) and see that the page title is correct (File manager page was titled “File Manager” but held some other none admin content and NOT the file manager module itself)
My next step was to see that the other content was doubled: in the original page and in the admin page. So I deleted the module from the admin page and put file manager as a module there.
Did the same for Event viewer page and Site log page. (other “old” admin pages were OK)
The only page I can’t find a way to fix is the Security roles page. I can’t find the module in the list nor in the modules definitions and I know the security roles are not a regular module so this is expected.
I hope I am more clear now.
BTW, with connection to our other discussion about friendly urls, the fact that the new v544 site did not apply human friendly urls and showed me the tabid’s help a lot.

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Yehuda Tiram
AtarimTR

972-2-5700114   |   972-54-4525492   |    http://www.atarimtr.co.il

You’re right about the upgrade and I had many sites upgraded from 4+ to 5+ but in this particular site the original was v3.3 and it could not pass the upgrade to 5+  for unknown  reason so I had to use the import (I used your suggested upgrade path and 495 was the last it could manage)

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Yehuda Tiram
AtarimTR

972-2-5700114   |   972-54-4525492   |    http://www.atarimtr.co.il