Is MRTG even running through your config file? Have you verified you have no major errors in the .cfg's that would possibly stop it from getting to that networking device? How many networking devices + ports on those devices are you monitoring that were set up with this wizard? What is the output of:
There are no major errors in the .cfg file. We are monitoring around 50 devices and all the ports. The port count varies from device to device from 2 to more than 30 ports.
Below is the output for "/usr/local/nagios/bin/nagios -v /usr/local/nagios/etc/nagios.cfg"
[root@localhost ~]# /usr/local/nagios/bin/nagios -v /usr/local/nagios/etc/nagios.cfg
Nagios Core 4.0.7
Copyright (c) 2009-present Nagios Core Development Team and Community Contributors
Copyright (c) 1999-2009 Ethan Galstad
Last Modified: 06-03-2014
License: GPL
Website: http://www.nagios.org
Reading configuration data...
Read main config file okay...
Read object config files okay...
Running pre-flight check on configuration data...
Checking objects...
Warning: Service 'Uptime' on host '172.21.41.249' has a notification interval less than its check interval! Notifications are only re-sent after checks are made, so the effective notification interval will be that of the check interval.
Checked 3765 services.
Checked 55 hosts.
Checked 8 host groups.
Checked 1 service groups.
Checked 3 contacts.
Checked 2 contact groups.
Checked 118 commands.
Checked 9 time periods.
Checked 0 host escalations.
Checked 0 service escalations.
Checking for circular paths...
Checked 55 hosts
Checked 0 service dependencies
Checked 0 host dependencies
Checked 9 timeperiods
Checking global event handlers...
Checking obsessive compulsive processor commands...
Checking misc settings...
Total Warnings: 1
Total Errors: 0
Things look okay - No serious problems were detected during the pre-flight check
Was this a new install starting at 2014r1.3 or did you upgrade? If you upgraded, which version were you running before?
Also, was this a system you configured and then installed Nagios XI from source or was it one of our VMs? If you installed from source, what OS/version are you using? Was it a minimal install?