KDE will autostart programs added to sessions in Gnome. The files are located in ~./config/autostart like the OP mentions. It is possible to disable the entries in "system settings/advanced/autostart" in KDE4, BUT this will edit the files in ~./config/autostart and thereby remove the entries from Gnome sessions.
So in short. I have the exact same problems. For more details see the first link posted by Adam Williamson.
KDE will autostart programs added to sessions in Gnome. The files are located in ~./config/autostart like the OP mentions. It is possible to disable the entries in "system settings/ advanced/ autostart" in KDE4, BUT this will edit the files in ~./config/autostart and thereby remove the entries from Gnome sessions.
So in short. I have the exact same problems. For more details see the first link posted by Adam Williamson.