Please describe the problem:
I have two keyboard layouts configured in gnome: normal QWERTY and Dvorak. When QWERTY is first layout on list, but Dvorak is actually selected one and I'm pressing ctrl+d (ctrl+h according to label printed on key) it should produce ^D (EOF) and window should be closed but it produces ^H (backspace). 

Steps to reproduce:
1. In Gnome Keyboard Preferences set up two layouts some QWERTY and Dvorak, put QWERTY as first one.
2. Select Dvorak as actual layout (using Keyboard Indicator Applet)
3. Open gnome-terminal. Press key labeled H (according you have qwerty labels). 
4. Press ctrl+H.

Actual results:
It prints "d" in step 3.
Then deletes it in step 4.

Expected results:
It should close terminal in step 4.

Does this happen every time?
Yes.

Other information:
It happens with all keys. d/h is only one example.