12.10 and Win7 on two disks problems

My Acer desktop was running Win7 on one disk and 12.04 on a second disk with additional ntfs partition.
I disconnected the Windows disk to install 12.10 ( I have learned the hard way with 12.04 that Ubuntu often wipes other OS unannounced)
Ubuntu offered to replace the existing 12.04 so I clicked Ok and it then erased the whole disk including ntfs and installed clean - not my definition of "replace". I notice I now have a UEFI partition.
Reconnected the Windows disk and did some Ubuntu updating - so far so good.
Next day I can only boot Windows and if I disconnect the Windows disk I get prompted for boot media. I can get back into 12.10 by booting from USB and chroot, but there does not seem to be a stable way to get something into the MBR

I know I personally just make a / partition and a /swap partition on my hard drive so it's easy to install any distribution I
want by just choosing the advanced setup and wipe the / partition and just have it install there.
By anyway, the day you were able to use Ubuntu and Windows - did it display the GRUB boot-loader or the Windows one?

The GRUB bootloader.
This PC can change disk priority by itself if disks are disconnected, not a problem with GRUB using blockid instead of /dev/sdx

I suspect GPT and EFI is the problem