Can't use 2 pins together on a single IDC connector (Altera DE1 Development Kit)

If I try to compile case C, on Quartus 12sp1, I get some warnings:

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Warning (275080): Converted elements in bus name "GPIO_1" using legacy naming rules. Make any assignments on the new names, not on the original names

Warning (275081): Converted element name(s) from "GPIO_1[1]" to "GPIO_11"

Warning (275081): Converted element name(s) from "GPIO_1[3]" to "GPIO_13"

Critical Warning (169085): No exact pin location assignment(s) for 2 pins of 4 total pins

Info (169086): Pin GPIO_11 not assigned to an exact location on the device

Info (169086): Pin GPIO_13 not assigned to an exact location on the device

--- Quote End ---

I don't use the schematic editor, so I'm not exactly sure what's going on, but it looks like Quartus is renaming GPIO_1[11] as GPIO_11, and the later name does not have a pin assignment.

My advice: stop using the schematic editor.