Comment 40 for bug 32194

This solution worked for me:

when you add programs to load at startup (from startup applications) some *.desktop files will be created at ~/.config/autostart. Now in order to change the startup order, you just need to rename those files (order them alphabetically as you desire). I tried giving them prefixes like 01XXX.desktop, 02YYY.desktop and etc. My problem is now solved but this might not be the total workaround.