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ArcGIS License Server Admin 10.1 status NOT RUNNING but is running

I have a problem with 10.1 License manager.

Once installed and authorized I have to alter the ports for firewall reasons. Once these ports are altered the status through the ArcGIS GUI displays NOT RUNNING.
Clicking on the start button does not do anything and the stop and re-read licenses remain grayed out.
On the Availability tab the licenses are shown, when viewing license usage it does not pick up that any are in use on the server.

However, there are no errors logged in the lmgrd9.log file and it shows that users are successfully checking licenses in and out.
On testing from other machines it is true that licenses can be checked in and out despite the apparent NOT Running status in the GUI. But it is not possible to view who is using them (or use the force checkin tool) other than through the lmgrd9.log file. From different Client machine Administrator's it is possible to see how many are in use.

The only way to start and stop the service is through the cmd line.

I have tested and when I reinstate the original default configuration of the service.txt file and use cmd line to stop and start the service, normal functionality of the administrator is resumed and it operates as expected with Status displaying RUNNING. But we cannot access licenses due to the firewall issues.

Is there anyway to fix this so that we have the intended functionality through the Administrator?

The machine the License manager is on is a VM running windows Server 2008 R2 Standard 64 bit operating system
It is the ArcGIS License Server Admin 10.1 with service pack 1
We have both Standard and basic licenses authorized
The Service.txt options are:SERVER this_host ANY 55000VENDOR ARCGIS PORT=55001INCREMENT ACT ARCGIS 1 permanent 1

From the lmgrd9.log:
18:48:52 (lmgrd) License file(s): C:\Program Files (x86)\ArcGIS\License10.1\bin\service.txt
18:48:52 (lmgrd) lmgrd tcp-port 55000
18:48:52 (lmgrd) Starting vendor daemons ...
18:48:52 (lmgrd) Starting vendor daemon at port 55001
18:48:52 (lmgrd) Using vendor daemon port 55001 specified in license file
18:48:52 (lmgrd) Started ARCGIS (pid 4764)
18:48:52 (ARCGIS) FLEXnet Licensing version v11.10.1.0 build 99220 i86_n3
18:48:52 (ARCGIS) Server started on Server_Machine for: ACT
18:48:52 (ARCGIS) Editor Viewer
18:48:52 (ARCGIS) EXTERNAL FILTERS are OFF
18:48:52 (lmgrd) ARCGIS using TCP-port 55001
18:51:24 (ARCGIS) TCP_NODELAY NOT enabled
18:52:51 (ARCGIS) OUT: "Viewer" user@machine

Anyone else experienced this? Any ideas on fixing this?

Thanks

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