If you're running an older version of the Community server then IBM support will probably tell you to upgrade it. It is documented in http://www.ibm.com/support/knowledgecenter/SSKTXQ_9.0.1/admin/upgrade/901_upgr_consider.html
that you should follow this sequence.
Upgrading DB2 is optional. Sametime 9.0.1 supports DB2 9.7 and later.
WebSphere Application Server
Sametime System Console
Sametime Community Server
Apply any IBM Domino® upgrade prior to upgrading the Sametime Community Server.
Sametime Proxy Server
Sametime Advanced Server
Sametime Meeting Server
Sametime Media Manager
Upgrade all Media Manager components in the same upgrade window to ensure all inter-dependencies are in sync.
Sametime SIP Proxy/Registrar
Sametime Video Manager
Sametime Conference Manager
Sametime combined PR+CF components
Sametime Video MCU
Sametime Gateway Server
As I have not done this myself I can't tell you whether it matters that the Community server is at an older version but there is every chance that the version of the Community server is being checked when you try to register the Gateway. By the way, is the SSC at version 9.0.1?
I really think you should upgrade the Community server before you burn too much time on this.
Are there any exceptions in the deployment manager and/or STConsoleServer SystemOut.log when you try to register it?