I was just pulling up a status export to check the SEPM for duplicate machines SEPM currently on 12.1.4023.4080. On the status export I can see a machine that has 19 entries same machine name same IP. When doing a full search from the clients My Computer on the machine name or the IP says it can't find any of the machines. Did a new status export same again can see the machine has checked in last 5 minutes but still nothing on the clients page. Says the client is on SEP 12 RU1 MP1. 

Anyone ever seen this before? 

If you go to the machine does it show connected as expected? Could be the duplicate HWID issue..

Repair duplicate IDs on cloned Endpoint Protection 12.1 clients

Duplicate hardware ID

Duplicate Hardware IDs result in only one client showing up in the Symantec Endpoint Protection Manager for multiple systems

http://www.symantec.com/business/support/index?page=content&id=TECH97626

We aren't even getting one entry but the report shows 19 in some cases. These are duplicate re-imaged citrix machines. They have to be manually deleted. 

Have you followed these steps:

How to prepare a Symantec Endpoint Protection 12.1.x client for cloning

Yes these steps have been followed but doesn't work for a citirix machine being returned to a standard image. Already raised a casue with symantec and they confirmed. 

But with this issue machines that are appearing in the status export aren't apperaing when we go into clients and search for the individual machines says they can't be found even though the status export can see them and they have checked in a few minutes ago. 

Since you're running old versions, could be a known issue. Would need to go thru old release notes to confirm or perhaps Symantec already knows.

run this query against DB and see how many show up

https://www-secure.symantec.com/connect/articles/how-find-duplicated-hardware-ids-database