UEFI or BIOS?
I think that windows has been installed in bios mode (using ms-dos partition table) and when you have updated the bios and then installed motherboard drivers have enabled gpt (using efi partition table) and your hardware has not been signed. So you can not boot because you have activated a new feature which is basically doing its job in preventing os starting. (i.e. bios has changed) Have you checked bios settings to load optimal defaults files and save and exit!? Check bios flash instructions.
Switching any installation from efi to bios or bios to efi is well recorded problem. Different motherboard manufacturers use different mechanisms to try and achieve switchability.
It should be possible to recover windows if you can get the appropriate efi/boot files in to the right place. After reading up here http://www.ecs.com.tw/ECSWebSite/Product/Product_Detail.aspx?DetailID=1228&CategoryID=1&MenuID=103&LanID=0 you should be able to get the relative information in order to check your BIOS settings are set appropriately.
It is recommended to get bios files directly from manufacturer.
It may be worth your while to confirm which bios file you installed and which bios file is being used. POST screen at reboot should confirm which bios version is being used. If you do not get POST screen try doing a clrcmos to reset bios back to version as motherboard left factory with. I had to adjust settings which are hidden in bios settings(check your mobo manual)-disabling logo and adjusting delay for checking harddrive are the settings that i changed in order for me to check which bios version is being used in order to help confirm flash was good on my new mobo.
A fresh installation may also be an option after checking your BIOS settings!?
You could try booting a ubuntu 12.10 live session dvd to use boot-repair to check your current disk partition table and getting a boot info script which will point you in the right direction for getting things going. Installing and running boot-repair recommended fix may even fix things for you to get booting again. Using gparted (from ubuntu live cd)to make a new parttion table and edit partitions will make ready your hdd if a fresh install is decided on.(after making sure your bios settings are appropriately set but you have to decide EFI or BIOS first? - or auto!?)
One week ago i did not know what uefi was!? Do not worry it is fixable!?You have asked in a good place!? Just giving some friendly advice and would highly recommend you trying Ubuntu 12.10 -as this may be a good opportunity to do so!?
(Switching your hard drive to ahci (non legacy) mode may mean you need ahci drivers before ubuntu/windows does an efi install.!? Am in a similar situation as yourself just trying to encourage you to give ubuntu a try-which definetley works in bios mode lol!?)
Try starting from here https://help.ubuntu.com/community/UEFI
Loads of good advice for similar problems in the ubuntu forums http://ubuntuforums.org/search.php?searchid=88241949