I'm using lxsession 0.4.9.1 and if the file ~/.config/lxsession/LXDE/autostart exists the file /etc/xdg/lxsession/LXDE/autostart will be ignored. This is problematic because this file contains the main applications to start my desktop environment. A workaround is to use only one of these files with all entries.
I have figured out that for example this command isn't executed anymore: "@xmodmap -e 'keycode 66 ='". On lxsession 0.4.6.1 it is working fine. Maybe it is because of the single quotes and maybe it has something to do with this problem.
I have made some more tests and found the reason for the single-/doublequote problem. The problem is that lines in the autostart file are parsed literally. For example @firefox "www.google.de" will open Firefox with the address "www.google.de". I have tried to use a \ to escape the quotes but this doesn't work too. @firefox \"www.google.de\" will open Firefox with the address \"www.google.de\". It seems that a redirector to a file doesn't work too. It would be easier if the commands would be more executed like bash does it.
I'm now using lxsession 0.4.9.2+git20140216 and the bug that both autostart files will make problems is fixed. But the parsing problem does still exist.