It's not a bug, it's a specifically mentioned limitation with a fix provided.CTR Bootmanager since it's a full fledged manager with menu and worked just fine before.
Anyway if thats the problem, then there is still a bug in aurei.
http://www8.zippyshare.com/v/UioYD4Mt/file.html
Use the patcher provided pathchanger folder. Drag AuReiNand's arm9loaderhax.bin onto the exe, type in the path/name that you're using (for me, it's AuReiNand.bin) and voila.