Resolution:
Note: The issue has been fixed in TRA 5.6.1

The work around is to run the following SQL in the database:
    select * from &ltdomain prefix&gtmap where mapkey='tibcoadmin.database.password';
    update &ltdomain prefix&gtmap set value='XXXX' where mapkey='tibcoadmin.database.password';
For example:
    select * from aumap where mapkey='tibcoadmin.database.password';
    update aumap set value='XXXX' where mapkey='tibcoadmin.database.password';

Keep a copy of the select outputs, just in case of the need to revert the values.

Replace XXXX with the value of the parameter:
    tibcoadmin.database.password
from the file:
    [TIBCO HOME]/tra/domain/[domain name]/AdministrationDomain.Properties
having removed single back slash characters (\) which are used to escape the next character.

For example, if the value in the file is:
    tibcoadmin.database.password=\#\!zJcXKSnRqc3y046MwPKuFyFfjW2TXEj5
Then the updates to apply are:
    update admap set value='#!zJcXKSnRqc3y046MwPKuFyFfjW2TXEj5' where mapkey='tibcoadmin.database.password';
    update aumap set value='#!zJcXKSnRqc3y046MwPKuFyFfjW2TXEj5' where mapkey='tibcoadmin.database.password';