I am having trouble with my Windows. I am considering options but before I do this I want to back my files up. In the past I booted into Ubuntu using a USB drive and copied files off the hard drive when I couldn't boot. I am attempting this now, hoever, I see some files but I do not see the folder that would be "My Documents" or contain the files on my desktop.
Is there a reason I am not seeing these files? Do I need to do something else to see all the files on the HD?
No. If you can see some files on the hard drive but not others then it might indicate that there is a problem with the filesystem. Make sure that you change the view in Nautilus to show hidden files, but this is unlikely to be the problem.
You could try installing testdisk on Ubuntu on the USB and see if that can help you recovery the missing files. Check the partition and mount status of the NTFS partition(s) with the commands
sudo fdisk -l
blkid
mount
first so that you have a better idea what you are dealing with.
If you have an external drive that is big enough and has enough free space, you could make a bit copy of the internal drive and use testdisk to investigate the file system on it. This is SOP for data recovery, especially in cases where the drive may be damages or failing.
