lxsession doesn't pass the desktop environment parameter to lxsession-xdg-autostart, so when I try to use it with i3 for example (lxsession -s i3 -e i3) the OnlyShowIn setting in .desktop files doesn't work as planned, because lxsession-xdg-autostart always starts with the default desktop environment, i.e. LXDE.
http://git.lxde.org/gitweb/?p=lxde/lxsession.git;a=blob;f=lxsession/main.vala;h=3c93b1d18a8d015c9dada4c14d3b3ced532a0df2;hb=HEAD#l428
http://git.lxde.org/gitweb/?p=lxde/lxsession.git;a=blob;f=xdg-autostart/main.vala;h=464898e7a48ebe5867906bd8edd38e51a0270844;hb=HEAD#l45
http://git.lxde.org/gitweb/?p=lxde/lxsession.git;a=blob;f=xdg-autostart/xdg-autostart.c;h=031cdafa372d7984328e4a8b50d1816107da6fd1;hb=HEAD#l190
Thank you very much for reporting this.
Fix pushed into GIT sources, it should appear in next release.