Weird error when installing Ubuntu for dual boot with windows vista

Hi this is my first post and i hope its in the right place. A few months ago i tried install ubuntu 11 on a second hard drive (My main harddrive is running windows vista). I installed every thing correctly as per tutorials and just common knowledge. the installation went off without a hitch.(or seemed too) however when i reset my computer i could not boot from either harddrive. Obviously a boot loader issue because both OS installations were perfectly intact just couldn't boot them. So after getting really scared and i little research i restored my windows boot loader with a repair disc. The weird thing is i repeated this installation process 100% identical to my first attempt and it worked fine no boot loader problem. What the hell happend? why would it destroy the boot loaders one time and work fine another under the same conditions. Im asking this because i want to do the same setup on a different computer but im scared to death of this boot loader problem happening again or something worse. If any one has any ideas or advice please let me know

I am sure there is someone much more knowledgeable about this that will help you more directly with your issue, but I have a machine with several OSs on it and a fair amount of experience multi-booting. The one thing you are doing that I have never tried is mounting the separate operating systems on separate hard drives. I am wondering if that is causing some system angst. Have you thought about moving all of your data to your second hard drive and then partitioning your first hard drive and putting the multiple operating systems on the same drive? That is how I manage my system and it works swimmingly. Once you install Ubuntu on your second partition along with Grub2, you can always run update-grub and it will search for any operating systems and load them into your Grub menu. Then each time you boot it will let you choose which system you want to boot. The double bonus is that if your operating systems completely fail or you need to re-install, your data is always available on the second hard drive and relatively safe. Just be sure to format it NTFS so Windows and Lunux can both read it.

Hope that helps.

Thanks bonesTdog for your quick reply. Im actually farmiliar with partitions however my first hard drive (windows) is almost completley full and i was using a seperate one for my linux for storage space reasons. however i am considering a partition for my newer system cuz the harddrive is considerably larger (750gb) however i do have an extra 120gb sata drive that id like to use in it if i can figure out how to ensure the boot loader issue doesn't happen again. Again I thank you for your speedy response.