.Xdefaults still works for me. You may need the class name. To get that, I run
xprop |grep WM_CLASS
then click the mouse on the program in question, for example, urxvt. (I don't have LXDE on this).
I get back
Code:
WM_CLASS(STRING) = "urxvt", "URxvt"
WM_CLIENT_MACHINE(STRING) = "scott1.scottro.net"
WM_COMMAND(STRING) = { "urxvt" }
In this case, URxvt, rather than urxvt, is the class so I use that name in .Xdefaults.
See if using the class name makes a difference--it will be the second name in the WM_CLASS(STRING) line, I think. I've never quite figured this out, but in openbox, for example, when one uses either application name or application class, if choosing class, one uses the second name in that line