Thank you for the quick response!
What distro are you using?
Dual-boot with Windows Vista and Ubuntu Gutsy Gibbon.
What filesystem are you/do you want to use?
My two existing Windows partitions (one for the OS/data and one for the recovery disk) are NTFS. My Linux partition(s) reside on the extended partition and are formatted ext3, except for one that is a swapfile.
Are you using a Dell box with software RAID?
I am on a Dell Vostro 1400. I'm using factory default settings, and I'm not sure how to check for RAID, but I don't think it's enabled, since my disk capacity is close to that of the physical limit.
Are you using your SATA drives in 3GB mode or 1.5?
Looking up my device name ST9160823ASG gives me the result that I am in 3GB mode.
Have you checked your partitions for errors?
I have run chkdsk on my Windows partition using the Windows Recovery CD; one bad file was found and fixed, and my C: partition is now in working order. I have not checked my Linux partitions, but they mount and run fine.
Using fdisk can be hazardous, as well as cfdisk.
What is your opinion on sfdisk?
Gparted is very reliable
I have used both a Gparted CD and a System Rescue CD to run the utility, as well as a copy of GParted I installed inside Ubuntu (obviously that copy isn't that useful, since the important filesystems are mounted when it runs). They all report that the drive is allocated.
Some more information after I did some testing:
sfparted reports two errors with my partition setup: the first is that the Windows volumes end and begin in partial cylinders. I believe this was the same way when I installed Windows, since from what I've read it seems not to respect cylinders. This would be, I suspect, the error cfdisk was complaining about. The second error is that the extended partition (/dev/sda4) extends beyond the physical boundary of the disk. This should be something I can easily fix; the last 1.5 GB of this extended partition is unallocated, but I can't figure out how to do an operation like this using the tools I have.
When I run parted, the command-line ncurses equivalent of gparted, it reports that it cannot fulfill all constraints on the partitions, and exits. When I run it and tell it to ignore errors, it gives the same view as Gparted.
As of right now, I've fixed the Grub bootloader so it now displays the menu (since the fdisk reordering changed drive names, grub was looking in the wrong spot for the linux kernel), and Windows and Linux booting works. As it stands:
1. I can read /dev/sda using fdisk (no errors), sfdisk (two errors) and Windows Computer Management (all healthy)
2. I get an empty allocation for /dev/sda using parted, gparted
3. I cannot read /dev/sda with cfdisk
4. Both Windows Vista and Ubuntu boot
Additionally, Sun xVM VirtualBox still reports that my partitions overlap (the original problem that prompted me down this path of partitioning mess).
Are there any other partitioning tools you recommend I look into for getting these problems fixed? Also, if I end up having to repartition my drive from scratch, what would you recommend I use to perform a full backup of my OSes, applications and data? (I would prefer not to have to recompose them from scratch).
I'm currently booted into Vista; shortly I'll boot into Ubuntu and give you the output of fdisk and sfdisk.