[adiadi]

Also tried to program alt+F4 on my harmony remote (that I am using downstairs, upstairs I have a cheap chinese MCE remote) but can't get this to work as well..

And tried to remap some keys with LM Remote keymap, but this did not work as wel..

Maybe one of the things that I have tried is interfering with the other, I don't know, but it is starting to get annoying

Haven't read the entire thread, maybe you already fixed this. It worked for me after disabling the MCERemote addon.
Make sure the key you program onto the Harmony is linked with the proper activity and/or device.