iarcherz, DarkSable,
Very similar, almost the same, problem just happened to me (within the last hour), and I fixed it solo before finding this post. Here's what happened:
I have a brand new tower, 4 days old, with a Panasonic 120GB SSD for windows and intensive games, and a 2TB Seagate for storage and downloading. (Model numbers omitted, but new OEM.) While I was at work, I think there was a power interruption hard-reboot at home. I got back to find the same 'bootmgr missing message. Repeatedly.
Here's what I did (that worked):
Before swapping out the SSD to either of the 2 SATA slots working, I re-flashed the BIOS. I turned off the 'Automatic' SATA detection, enabled the post-SATA functionality option (name forgotten already, but the hierarchy is IDE->SATA->post-SATA-Advanced-Something-4-letter-acronym), I re-detected the drives, and swapped the boot order so the SSD was first again.
Nothing lost (Google chrome even remembered my open websites), and no fiddling inside the case. But DarkSable has a good suggestion - always keep a backup of (any-even back to XPSP3) old windows on CD (not DVD) in case your system fracks up. Same file will fit on a 1GB memory card, but then required USB2.0+ to handle it.
Hope anyone else with the same issues solves them tickety-boo.