Now it is more clear

Probably a corrupted config (/home/user/.desktop_cmd_exex)?
I once had to start anew, too (do not remember whether after fiddling with it or just out of the blue.

Best would be to check that file after deleting all.all.commands (it should be empty, or almost empty).
I may attach a original 'blank' file a bit later ...
... and here it is (gzipped)