Query builder subquery added multiple quotes if select more than 1 column

Your issue with quotes.
I think that's the normal behavior of CI $this->db->from()

Look the fille system/database/DB_query_builder ligne 478. there is an explode function in the parameter of from.
After that, you have an array:

(SELECT trx_no
pendaftaran_id FROM t_transaksi GROUP BY
trx_no
pendaftaran_id) as t_tr

line 483: each row of the array go to function protect_identifiers...: you find it in DB_driver line 1782.
In this function you find line 1833 a condition: if the string contains a parenthesis or ' return the string without quotes.

Finally, you can't get the correct query....

Sorry for late answer.
Oh yup, that's my problem.   

Thanks for your help.