Steps to reproduce:
0) Compile the attached testcase
1) rm -f ~/.local/share/applications/gedit.desktop
2) Associate text/plain files with gedit ("Text Editor") in nautilus
3) run the testcase with an existing file, like so: "./test test.c"
4) Right-click on any file in nautilus, choose "Open with other application"
5) Expand "Use custom command", enter "gedit --new-window" (without quotes)
6) do (3) again

Expected results:
Step 3 and 6 launch gedit, opening the file given as argument.

Actual results:
Step 6 launches gedit with a blank document.

Further analysis reveals that in step 3, the desktop file associated with the
default handler for text/plain is /usr/share/applications/gedit.desktop, while
in step 6 it is ~/.local/share/applications/gedit.desktop, even though you
didn't change the default handler! That desktop file has the Exec line
"Exec=gedit --new-window"; note the absence of %U like in the system
gedit.desktop file.

GNOME-VFS 2.9.92, Nautilus 2.9.92 (ubuntu hoary).