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I believe I've solved the problem. What you need to do is:

1. Go into System Preferences - Keyboard - Keyboard Shortcuts - Services.

2. Scroll down and Find the OmniFocus: Send to Inbox entry.

3. *Uncheck* the box beside the entry.

4. Close System Preferences.

5. Open OmniFocus and go to Preferences - Clipping.

6. Enter the shortcut you prefer (ctrl + shift + comma worked for me).

My guess is that there is a bug preventing you from changing (or creating) a shortcut in OmniFocus while the box is checked in System Preferences.