Try assigning it manually:

Assign Ctrl+Enter shortcut to AutoCode.Execute command
1. On the Tools menu, click Options.
2. Expand the Environment folder, and select Keyboard.
Note: If you do not see the Keyboard page, check Show all settings located in the lower left corner of the Options dialog box.
3. In the Show commands containing box, enter “AutoCode”.
It will show AutoCode.Catalog and AutoCode.Execute commands
4. Select AutoCode.Execute
5. On the Use new shortcut in drop-down list, select Global.
6. Place the cursor in the Press shortcut key(s) box, and then press Ctrl+Enter
7. Check the Shortcut currently used by box to see if the key combination is already assigned to another command. If so, follow the directions bellow to remove the conflicting shortcut.
8. Click Assign.

Remove conflicting shortcuts
By default, Ctrl+Enter shortcut is used for the Edit.LineOpenAbove command (not very useful command). To remove this shortcut and let Ctrl+Enter be correctly assigned to AutoCode follow these steps:

1. On the Tools menu, click Options.
2. Expand the Environment folder, and select Keyboard.
3. Place the cursor in the Press shortcut key(s) box, and then press Ctrl+Enter
4. Check the Shortcut currently used by box to see which command or commands use Ctrl+Enter shortcut
5. If there are other commands other that AutoCode remember the name of the command or commands (probably Edit.LineOpenAbove command)
6. In the Show commands containing box, enter the name of the command
7. Select the command
8. Click Remove.
9. Repeat step 6 for any conflicting command (but not for AutoCode.Execute command)

There is a Microsoft article How to: Work with Shortcut Key Combinations for more information about shortcuts.