Ubuntu :: Rsync Copy Results In Incomplete File

Using Ubuntu Server 10.04 LTS. I'm new to Ubuntu and testing Rsync. I successfully copied 3TB of data from a Win7 machine to an MDADM Raid5 array. All appears to be fine. Used a Win app for the copy. I then deleted a 250GB folder on the Raid5 array and recopied the data using Rsync. Rsync was executed via a Putty session on a WinXP machine. The source was an eSata attached drive (same drive used for the big 3TB copy) and the destination was the same Raid5 array. That copied just fine. I bit verified it with a Win7 app. Perfect.

I then used the following Rsync script to copy a single 26GB file from that same eSata drive back to (what I intended to be) the Raid5 array:
Code:
neil@ANTECUBSV:/mnt$ rsync -r -a -v -e ssh --delete /mnt/disk1/Test/ /mnt/Test
sending incremental file list
created directory /mnt/Test
./ C_VOL-S300-b001.spf
sent 3020267622 bytes received 34 bytes 50760800.94 bytes/sec
total size is 3019898880 speedup is 1.00
neil@ANTECUBSV:/mnt$ cd raid

Note that only about 3GB copied. No error messages were posted to the putty session. I made a mistake in the Rsync command, creating the Test folder directly in the mount folder rather than the Raid array, as I intended. That is a little strange, yes, but I would not think it would cause a partial copy? The /mnt folder is on my system drive, which had about 34GB available space before the copy, so comfortably would have had 6GB or so after.
The eSata disk is mounted as /mnt/disk1
The Raid5 array is mounted as /mnt/raid

I then recopied the file to the correct intended destination on the Raid5 array, which has about 400GB free space (plenty).
Code:
neil@ANTECUBSV:/mnt/raid$ rsync -r -a -v -e ssh --delete /mnt/disk1/Test/ /mnt/raid/Test
sending incremental file list
./
deleting 2010-07-05 Backyard Birds/Thumbs.db
deleting 2010-07-05 Backyard Birds/
C_VOL-S300-b001.spf
sent 11105775462 bytes received 34 bytes 50366328.78 bytes/sec
total size is 11104419840 speedup is 1.00
neil@ANTECUBSV:/mnt/raid$ df -h

Note that only about 11GB was copied, and this was confirmed with an ls -l command. Now I am correctly copying the file to the Raid array but it is still incomplete. I then copied the file back to the /mnt folder to see if the problem reproduces:
Code:
neil@ANTECUBSV:/mnt/raid$ rsync -r -a -v -e ssh --delete /mnt/disk1/Test/ /mnt/Test
sending incremental file list
created directory /mnt/Test
./
C_VOL-S300-b001.spf
sent 26327927554 bytes received 34 bytes 56558383.65 bytes/sec
total size is 26324713984 speedup is 1.00
neil@ANTECUBSV:/mnt/raid$ cd /mnt/test

This time I got my full 26GB file. Why I might be getting inconsistent results? This is quite troubling of course. I'd also be interested in basic a command line Linux diff app (that does file directory as well as bit level checking) if one is available.