Ok, it's all works now. I traced the issue to some hotfixes I added long time ago , that ended in svcpack folder.
However when I update some hotfixes they appear in .exe format in svcpack folder instead as .ca_ files (catalog files) , when I look inside I see that they are in form of sfx packed package.
When I start the mentioned hotfixes , a temp file is generated on hd, having the normal dir structure as a normal hotfix package.
How can i add this files to be integrated normally as other hotfixes (so they leave just .ca_ file in svcpack folder)?
When I try to repackage the extracted hotfix back to .exe so nlite can use it, it fails to integrate, so how can I repackage them in this normal folder structure way?
Also if I choose to use ryanvm post sp3 update pack to update windows, can I use nlite after/before that integration, or is not advisable?