If you check Spotfire server logs, you can see below type of errors in server.log file:
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ERROR 2018-09-26T07:29:04,380+0200 [sfadmin, #48, #274] server.security.RoleManagerImpl: Internal error when looking up administrator privileges for user 'sfadmin[2689a4a5-61a2-402b-a928-e8cb4ac6804e]' in the UserDirectory
...
...
Caused by: com.microsoft.sqlserver.jdbc.SQLServerException: Invalid object name 'GROUP_MEMBERS_VIEW'.
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WARN 2018-09-26T08:54:25,567+0200 [monitoring@SPOTFIRESYSTEM, #54, #144] ws.userdir.UserDirectoryService: An exception was thrown in method 'getGroupsRecursive'.
com.spotfire.server.userdir.DirectoryException: Failed to load group membership associations from database
...
...
Caused by: com.microsoft.sqlserver.jdbc.SQLServerException: Invalid object name 'GROUP_MEMBERS_VIEW'.
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ERROR 2018-09-26T09:16:21,188+0200 [sfadmin, #57, #2237] server.security.RoleManagerImpl: Internal error when looking up administrator privileges for user 'sfadmin[2689a4a5-61a2-402b-a928-e8cb4ac6804e]' in the UserDirectory
com.spotfire.server.userdir.DirectoryException: Failed to load group membership associations from database
    at com.spotfire.server.userdir.MSSQLDatabaseProvider.getParentGroupsRecursive(MSSQLDatabaseProvider.java:203) ~[server.jar:?]
...
...
Caused by: com.microsoft.sqlserver.jdbc.SQLServerException: Invalid object name 'GROUP_MEMBERS_VIEW'.
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These errors indicates that there is some issue with group membership in Spotfire Database which may be causing this issue.

After Spotfire server upgrade, when Spotfire Administrator user log on to Spotfire server URL can only see "Home" and "Analytics" options and no other options are visible.

Points to check to resolve this issue:

1. Check the user permissions on Spotfire Database by which you ran Spotfire server upgrade tool. Check if this user has proper permissions(For example: CREATE SESSION,CREATE TABLE, CREATE PROCEDURE, CREATE VIEW, QUERY REWRITE) on Database views for which you are getting errors in logs.

2. Check if your Spotfire database equipped with integrated security. If yes, make sure that you checked this integrated security option while running Spotfire server upgrade tool.

3. Check if Database views for which you are getting above errors in logs, are get created properly in Spotfire Database. If not, you may need to create these Database views under Spotfire Database user again with the help of your DBA.