Version: 1.3.1 - 1.3.1-700-g138ffc16 (master
https://gist.github.com/fogine/987e98b48ebf0df76a1a8f5f10d5fdb7
rofi -show window -kb-row-down "Control+j"
Also fails with .Xresources option: rofi.kb-row-down:Control+j,Down,Control+n
This behavior applies for all user defined bindings.

Rofi fails to start with an error: "There is already a binding matching Control+j".. (hand written, not copy pasted).
Rofi launched with keybindings mapped.
The behavior is correct. you cannot bind two action to one key-combo.
To find out, which setting you need to unset use
rofi -dump-xresources | grep Control+j | awk '{ print $2 }'
Then simply set it to nothing.
Example:
rofi -dump-xresources | grep Control+j | awk '{ print $2 }'
rofi.kb-accept-entry:
rofi -kb-accept-entry "" -kb-row-down "Control+j"
Thank you @carnager , I got confused as in previous versions of rofi I didn't need to unset the bindings. I guess some new default bindings were added since then. My bad.
In previous versions it indeed did not throw an error. It would bind the key twice, and the first one in the list would trigger. So depending where your binding was in the list you would trigger one or the other.
This non-deterministic behaviour is even worse 馃檨 .
@DaveDavenport Why command line options hasn't higher priority than configuration files? I want to use rofi as interface of my script, but I can't be sure that my keybindings not already used in user config.
@hxss please follow the guidelines and open a new issue. Do not hijack issues.
Most helpful comment
In previous versions it indeed did not throw an error. It would bind the key twice, and the first one in the list would trigger. So depending where your binding was in the list you would trigger one or the other.
This non-deterministic behaviour is even worse 馃檨 .