Windows Vista recovery

#1
I have a dual booted laptop that will not boot.
Here's the summary:
1 Vista boot partition
1 Vista data partition
1 main Ubuntu partition
1 Ubuntu swap partition.

I can boot Ubuntu, but not Vista.
The problem happened when I was running Vista and removed the Intel Matrix Storage Manager (long story).
After that, Vista would not boot. I'd get a prompt to recover or continue with normal boot.
Both would restart the computer after a couple seconds.

So, I bought the NeoSmart Vista CD. I can boot from it, and it lists all the partitions.
However, when I choose the automatic recovery (I don't remember the exact names of the choices),
it lists the "eligible" partitions, but only shows the Vista data partition.
I can start gparted and can see the Vista boot partition.

Why would the boot partition not be eligible?

I booted back into Ubuntu and ran boot-repair.
Its output is at:
http://paste.ubuntu.com/1422525/

The weird thing is that it lists the Vista boot partition as:

sda1:
__________________________________________________________________________
File system: ntfs
Boot sector type: Windows Vista/7: NTFS
Boot sector info: No errors found in the Boot Parameter Block.
Operating System: Windows Vista
Boot files: /bootmgr /Boot/BCD /Windows/System32/winload.exe

and then later lists it as FAT16:

Partition Boot Start Sector End Sector # of Sectors Id System/dev/sda1 * 26,619,904 326,080,511 299,460,608 6 FAT16
/dev/sda2 326,080,512 618,199,391 292,118,880 7 NTFS / exFAT / HPFS
/dev/sda3 618,201,086 1,465,147,391 846,946,306 5 Extended
/dev/sda5 618,201,088 1,456,762,879 838,561,792 83 Linux
/dev/sda6 1,456,764,928 1,465,147,391 8,382,464 82 Linux swap / Solaris

Any ideas what is going on? What is my next step?