Same problem here,
Currently on stock 4.3 version, even tested with 4.2.2(previous version)
I m not able to configure my FastWay Hd Set Up Box remote by manual method..
It didnt work on STB...
Only default configured codes are working Like SonY Led Remote and Samsung
if I was able to help you.
Device: Sony Xperia ZL - Stock Rom 4.3
Device: Sony Xperia Mini Pro SK17i(Mango) - JB 4.3 [CM10.2]LegacyXperia
[Happy to help]