The only thing I know for sure is that it's not something that was introduced by Sigil 2.7.0. I suspect that something has changed in Arch with respect to XDG and Free Desktop. I also know that .desktop files that are not kept in standard locations (/usr/share/applications, /usr/local/share/applications, and ~/.local/share/applications) can behave weirdly.
My advice at this point is to keep everything standard and put your custom .desktop files in /home/ruben/.local/share/applications to simply override the system installed defaults (instead of creating them on your desktop), or just continue to put the explicit path to Sigil's launch script (/usr/bin/sigil) in your custom .desktop files and be done with it. I fear something is broken/misconfigured on your system that I just can't figure out without getting my hands on it.
