Duplicate channels means you have installed an out-of-region update at some stage. If those channels have dissapeared now then it might have been corrected by your system update. The solution to Semi-brick is to install an updated system menu, which you have done already.
v289 won't work because it's for a 3.2U system when you have 4.1 installed.
Try formatting your SD card (backup the files first) and going through those channels again. There might be some files on your SD causing the lockup.