I know this is an old thread, but I ran into this subpicture alignment problem early on and overcame the problem easily.
For me, the alignmment problem occurred when I used the “subpicture button” in the button properties window. This should be the simple and obviously best way, but not with the misalignment. Also, the problem occurred when I had already set up a stroke on the text (not the drop shadow). So, I merely make sure I use the Object menu to set up the subpicture (Ctrl-Alt-B shortcut) before I apply my stroke and drop shadow.
In summary, no problems if I follow this sequence–Subpicture first from object menu or shortcut keys, then stroke and dropshadow.