New DB is not in the end user list
I don't see how it is possible for tom to have sysadmin rights and not see a database.
Does tom still have sysadmin rights with with the new version of SSMS?  Normally refreshing or closing and re-opening SSMS is all that is required
Are you sure he is connecting to the correct server?  Sometimes there is a dev or test server with a similar name that the user also has rights on, but is not the same as the one you are working on.
The normal cause of the situation you describe is that 'tom' (assuming 'SQL Server login' as apposed to a windows account) has a different SID in one scenario than in the other.  This is corrected by using
SP_CHANGE_USERS_LOGIN
sp_change_users_login (Transact-SQL)
If you can go to his desk and look over his shoulder OR if he will screen share; you should see where he is doing something different then you are doing when you log on with what you believe is the same account.
Another test is you can use sp_who to see if tom is actually logged on to the server you think he is.