FIXED! 
Don't know if it was a permissions issue or one of these two services not running:
# service ndo2db stop
Stopping ndo2db: head: cannot open `/usr/local/nagios/var/ndo2db.lock' for reading: No such file or directory
done.
# service nagios stop
Stopping nagios: /etc/init.d/nagios: line 67: kill: (2930) - No such process
done.
Steps taken:
1. Followed the pdf "Nagios XI – Fixing Global Permissions.pdf" = still wasn't working (although, don't know if I had to let Nagios catch up, but I thought 10 minutes was long enough)
2. Something that has worked for me in the past was to simply run the upgrade process script again; However, I didn't have to go all the way to the "./upgrade"
service nagiosxi stop
service npcd stop
service ndo2db stop
service nagios stop
mkdir /root/pre-upgrade-backup
tar cjf /root/pre-upgrade-backup/usr-local-nagios.tar.bz2 /usr/local/nagios
tar cjf /root/pre-upgrade-backup/usr-local-nagiosxi.tar.bz2 /usr/local/nagiosxi
pg_dump -U nagiosxi -c -F p nagiosxi | bzip2 -c > /root/pre-upgrade-backup/pg_nagiosxi.sql.bz2
mysqldump -u root -pnagiosxi nagios | bzip2 -c > /root/pre-upgrade-backup/my_nagios.sql.bz2
mysqldump -u root -pnagiosxi nagiosql | bzip2 -c > /root/pre-upgrade-backup/my_nagiosql.sql.bz2
service nagios start
service ndo2db start
service npcd start
service nagiosxi start
Once I got to this point, I checked NagiosXi and the services that were labeled "Pending" before. I did a "Schedule an immediate check" and they were all now being checked normally.
Conclusion:
Don't know if it was indeed a permissions issue (which looks like its a normal factor when ever I have a problem with NagiosXi), or if service "ndo2db" was not running properly.
Thanks for all the support on this, as I couldn't have fixed it without your help.
Eddie
PS: I'm putting together a troubleshooting list, for when I encounter similar problems. List as follows:
Troubleshooting Steps:
***1. Check to make sure the following are running:
service nagios start
service ndo2db start
service npcd start
service nagiosxi start
**2. Fix Permissions:
reset Nagios permissions and ownerships:
# /usr/local/nagiosxi/scripts/fixperms.sh
This command will fix your permissions, but after this you have to run:
# chown root.nagios /usr/local/nagiosxi/scripts/reset_config_perms
# chmod u+s /usr/local/nagiosxi/scripts/reset_config_perms
# chown root.nagios /usr/local/nagiosxi/scripts/reset_config_perms.sh
# chmod u+s /usr/local/nagiosxi/scripts/reset_config_perms.sh
And finally:
# service nagios restart
# service httpd restart
/usr/local/nagiosxi/scripts/reset_config_perms
**3. Fix Global Permissions:
Follow the pdf "Nagios XI – Fixing Global Permissions"
/usr/local/nagiosxi/scripts/
./NagiosXI-FixPerms.sh
The script will run and may show a few errors. This is normal, some files may not exist on your system
**4. Run the NagiosXi upgrade script
service nagiosxi stop
service npcd stop
service ndo2db stop
service nagios stop
mkdir /root/pre-upgrade-backup
tar cjf /root/pre-upgrade-backup/usr-local-nagios.tar.bz2 /usr/local/nagios
tar cjf /root/pre-upgrade-backup/usr-local-nagiosxi.tar.bz2 /usr/local/nagiosxi
pg_dump -U nagiosxi -c -F p nagiosxi | bzip2 -c > /root/pre-upgrade-backup/pg_nagiosxi.sql.bz2
mysqldump -u root -pnagiosxi nagios | bzip2 -c > /root/pre-upgrade-backup/my_nagios.sql.bz2
mysqldump -u root -pnagiosxi nagiosql | bzip2 -c > /root/pre-upgrade-backup/my_nagiosql.sql.bz2
service nagios start
service ndo2db start
service npcd start
service nagiosxi start
cd /tmp
wget
http://assets.nagios.com/downloads/nagi ... 1.7.tar.gz <---- remember to choose the latest Nagios release
tar xzf xi-2011r1.7.tar.gz <---- remember to choose the latest Nagios release
cd /tmp/nagiosxi
./upgrade
