The only thing I can think of is perhaps you need to run a chkdsk on the NTFS drive. Have you booted into Windows since resizing the partition? It will usually run chkdsk automatically when booting when it discovers the partition size has changed.
Yeah, I ran a chkdsk before re-partitioning, and once I partitioned, I booted in Windows XP and it automatically ran a chkdsk. I've booted into Windows several times since (and before trying to back up with CloneZilla).
Since Clonezilla didn't work, I tried my old backup software, Nero Backitup Essentials (a basic OEM version that came with my DVD-writer and runs in windows or from a bootable recovery CD). It's always worked well when backing up my Windows XP partition.
It also seems to recognize the file system on the linux partition (it shows a graphic diagram of the disk structure and identifies the Windows partion as NTFS, the Linux partition as ext3 or something (I can't remember)). It also identifies another undesignated 3GB partition on the disk (not sure what that is).
I've used it now to backup both the Windows XP and Linux partitions individually, and then the whole drive (imaging the drive).
Before backing Linux partition it does warn that since the partition doesn't have a Drive Letter, it can't lock the partition during backup. However it will still proceed and does successfully verify the backup image file against the real partition.
As I said, I've also used it to "image" the whole 160GB drive (Windows XP / Linux / undesignated partitions) all together. Since Nero Backitup is a Windows program, and I'm booting from the Windows XP partition, it warns again that it won't be able to lock the Windows partition as it is in use. But again, it backs up the whole drive. I know in the past when I've had to restore my Windows XP setup from these backups it has worked fine.
Nero Backitup Essentials is pretty easy to use and even allows the making of a bootable live restore CD (which I've done and had to use in the past).
So I hope I'm covered.