To gather schema statistics we have program in Oracle Apps (Gather Schema Statistics).
But when we select ALL as parmater to run gather schema , it will not consider the custom registered schema's and run gather stats for only default schema's.
 
 
 Concurrent –> Request –> Submit Request –> Gather Schema statistics (Paramerters “ALL”)
 
Reason:
Whenever Custom schemas are registerd in Oracle Applications , the entries are done in 2 tables
ie FND_ORACLE_USERID and FND_APPLICATIONS_TL

However , when Gather schema statistics is submitted it uses the below query to get schema information
select distinct upper(oracle_username) sname
from fnd_oracle_userid a,
fnd_product_installations b
where a.oracle_id = b.oracle_id
order by sname;

Note : When custom schemas are created the entry is not made in fnd_product_installations and hence it is not picked up in the above query.

Solution :

Make an entry in fnd_product_installations so that it is picked up by Gather Schema Stats. Follow below steps
Select Responsibility Alert Manager — > Systems –> Installations
Define custom application in this form , go the last record and make entry for custom applications. Once this is done , it will insert an entry in fnd_product_installations.
Submit Gather Schema stats and then query dba_tables and you will realize , stats are being gathered for custom schemas as well.