To my regret I have noticed the same issue.
I do have the same version installed and have 2 separate harddisks placed in my computer,
Both of them where individually installed with windows 7 and placed in there own bay.
I'd like to have the bootmanager skip the menu unless i need the other install, but i cannot change anything.
When i change the radiobutton to skip the menu and press save it tells me that the settings where saved but when i reboot the menu just appears and when i look to the settings nothing has changed.
I do like the bootmanager as it is very simple to use, but i do find it important for me that the menu can be switched off.
I can't see the point of having a dual-boot menu which you skip.
If you want one OS 99%, wouldn't it be simpler not to dual boot, and just boot the 1% option with a temporary BIOS override to the 2nd HDD if ever you require it ?
Nevertheless, missing those options probably indicates minor BCD corruption.
Try EasyBCD > Backup/Restore > Reset BCD and then DO NOT REBOOT until you've added at least one W7 entry back into the empty BCD.
All options should be available.