I was actually what i thought, i just had to find it:
I looked into the nagios log (<nagios folder>/var/nagios.log) as i was restarting the nagios service and i got the following line:
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[1354184763] Warning: Could not open object cache file '/usr/local/nagios/var/objects.cache' for writing!
Therefore the nagios process was not able to update the file with the new servers and thereby the web interface never got to see them!!
I fixed it by making nagios:nagios the owner of this file, and everything is working perfectly now!
Again, thank you so much for your help and that you took your time to read my long post's.. i am writing the solution hoping that someone else will find it if they have the same problem!