It's been discussed by this group, so I thought you'd be interested in a snippet from a reply I received from IBM, to a Q I asked regarding the whole Windows Terminal Server - MQ conflict issue:

"The Windows 2000 Terminal Server environment introduces the idea of
name spaces for kernel objects within the operating system.  The local
and global processes reside within one namespace, and clients and client
initiated processes reside in others.  Each client, when connected, is
allocated a namespace of its own, and the default behaviour for newly
created processes is to create them in this client namespace.  Processes
created in a client s namespace are not immediately accessible by other
clients, and therefore the client s namespace can be considered
protected and separate, as if the client is running on a separate
machine altogether from other clients.  Client processes can see the
global namespace.
.
The implication of this to IBM MQSeries is that the core processes such
as the queue manager itself, should be launched in the global namespace,
and not under individual client namespaces.  If the queue manager is
started by a client therefore, it will not be available to other
clients, or applications local to the server itself.  One of the reasons
for adhering to this model is to protect against processes being created
in temporary namespaces, which are only available for the duration of
the client connection.  (ie.  A client could log into the system then
start a queue manager; if the server had access to that queue manager,
they could start using it, but then, the client disconnects, and all
processes in that namespace are terminated - including the queue manager
that may be in use).
.
In practice, queue managers should be started either by the Windows NT
IBM MQSeries Service, by the MMC MQSeries Services snapin, or by a user
logged into the server machine locally.  The MQSeries Services snap-in
works in this scenario because the actual start command is executed
under the MUSR_MQADMIN user account, which is running in a local
namespace on the server itself.
.
There has been some discussion that MTS will be supported in MQSeries
5.3, but as of yet I don't have any confirmation.  Please be on the look
out for product release info that should be coming soon.

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