issues with mozembed and x reparenting

I am embedding mozilla in my X based application (ubuntu 9.10/gnome)
using mozembed and xreparenting (an xwindow is created by me, followed
by mozembed GTK widget and then the widget is reparented to the one I
created) and wanted to know if anybody here had done similar project.
I have some major issues with it, such as I must have to run my app
manually from a shell - I cant my application from init scripts even
after waiting for  X to finish loading and GDM stared, even after I
hardcoded the xpcom paths etc. Second major problem is that the
somehow sometimes a second window pops up with nothing on it which
obstructs the mozembed widget. This must be related to xreparenting.
Third major issue is the gtk_main that is needed for mozembed widget
eats up all the events including x events but I did see it passing
them back to its parent window handler - only at certain times as I
frequently destroy the app and restart. It might be related to that
other window popping up but I cant conclude.

Just curious if anybody has some insights. Thanks