I tried installing Ubuntu 9.04 for the first time-I am currently running a dual boot of Vista and XP on a WD SATA HDD(running as IDE)-call that Disk 0. I also had several other partitions on the SATA HDD containing documents, images, and so on. I also have a 250 GB WD IDE HDD(call that Disk 1) which at the time was blank and unformatted. I decided to install Ubuntu to Disk 1. The mistake I made was the following: I changed the HDD boot order in the bios to boot from Disk 1 first. I then booted to the Linux install disk and proceeded with the installation, which went fine. I had thought that when I rebooted, it would boot Linux from Disk 1-instead it found no operating system. I then changed the HDD boot order in the bios back to the way it had been- Disk 0, the SATA HDD listed first. I was then given the option of booting into Linux or choosing the Vista bootloader, which then enabled me to boot into Vista or XP as I had always done. So what’s the problem ? From within Vista, some of the partitions on Disk 0 (all formatted as NTFS) were not visible. Disk management showed the XP, Vista, and documents partitions. The rest was listed as free space and I couldn’t access the files. Fortunately, from within XP all of the partitions on Disk 0 were visible. However, both Partition Magic and Easeus Partition manager listed Disk 0 as bad, and none of the partitions were shown. Thus I cannot work with the free space on Disk 0. From within Linux, Disk 0 is just shown as all free space. What I don’t completely understand is why the Ubuntu installer would mess with any of the partitions on Disk 0 when Ubuntu was installed to Disk 1. Is it because I changed the HDD boot order in the bios to boot from Disk 1 first ?

My guess is that once you changed bios to select the boot order you may have confused what drive you wanted to load linux and more importantly you may not have had the chance to decide which drive you wanted to load grub on. I tend to like using boot order to save my current system. Most always works as it should. There are rare instances that happen when your MS system might be on what appears to be C: but really three or four files are really on another partition. Since you have a newer system, you might wish to play with virtual machines a bit. They should run fine on your system and you won't be messing up your bootloader. "Best Practices", Event viewer, host file, perfmon, antivirus, anti-spyware, Live CD's, backups, are in my top 10

Jefro: Thanks for the reply. I believe I did have the choice of which drive to load grub on. I'll have to wipe everything at some point and do this over again. From what I have read, it is better to install Linux after Windows, because Windows can mess with the Linux boot loader. However, it seems that Linux messed with Windows partitions in my case.