Issue with Agents in Application DNS domains

I have a confusing scenario. We have a number of servers being monitored that have their DNS in an application domain, not their true AD domain. When installing the SCOM agent it picks up the application domain FQDN (properties tab of the agent) and not
the true AD FQDN. The console shows the servers by true AD FQDN. The servers show up in the console as "Not monitored".
I have not found a config file or registry entry where I can change this. One option I thought of is to remove the explicit "Primary DNS suffix for this computer", install the agent, then put the application domain suffix back. That is a lot of
work, though.
Any other suggestions so I can get these systems monitored?
Thanks,
Steve

Hi,
We should check operation manager logs on the agent, and check out any related messages there, if there is no errors or warnings, then I would like to suggest you remove agent from the problemtic computer and clear caches, and then manually reinstall the
agent and check the result.
If the issue is still there, we may try your method.
In addition, also hope the below link be helpful:
Fixing troubled agents
http://blogs.technet.com/b/kevinholman/archive/2009/10/01/fixing-troubled-agents.aspx
Regards,
Yan Li
Regards, Yan Li

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2014 HR Block Premium Fed+State - Program crashed(Pay attention to steveu1`s answer )
http://community.hrblock.com/t5/DIY-Products/2014-HR-Block-Premium-Fed-State-Program-crashed/td-p/57634#.VL4ANHkfrwo
NOTE: This response contains a reference to a third party World Wide Web site. Microsoft is providing this information as a convenience to you. Microsoft does not control these sites and has not tested any software or information found on these sites.
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