Multi-server administration - force poll on target fails, server needs to be registered locally without FQDN
I know it's been a while, but I have the same issue trying to manage multiple domains. (Avoid using the same server name in more than one domain.)  The Multi-server feature seems to be very limited, but it could be so much better with a little effort.  I figure it will be removed from the product one of these years, fixed, and then added back as a great "new" feature in the ENT edition.  

I think the limitation is in the extended procs such as xp_msx_enlist code.  They determine the name of the local instance.  If it was T-SQL code, it might have been easier to fix.  As far as I can tell, the only place the target name is stored is in msdb.dbo.systargetservers table on the master server.  If the targets could be tricked into requesting a sync for the FSDN, then the table could have be updated (hacked) directly to use the FQDN.  

If it was open source, it would have been fixed years ago.  It would have had more features by now too.