This is very important! TrueCrypt system encryption partition DOESN'T CONTAIN TRUECRYPT HEADER. Non-system Truecrypt encrypted partition or file container contain header at first 128 blocks and backup copy at last 128 blocks of file/partition. So it's to impossible to decrypt systen encryption partition without backup header. Header of system partition is at the last block of hdd's first track. You can backup header:
dd if=/dev/sdx of=header.img bs=512 count=1 skip=62
If you want to access partition backup you have to clone partition to same size primary partition to different hdd and mark it as bootable. Then you have to restore header. First check if the first track is empty:
sfdisk -l /dev/sdy
If first partition strats at block 63 or more it's ok but if it's lower block number you can't continue.
Restore your header
dd if=header.img of=/dev/sdy bs=512 count=1 seek=62
The you can access your backed up system partition using "Mount partition using system encryption without pre-boot authentication".
Theoretically you can convert Truecrypt system partition to standard Truecrypt parition or file container but you would have to chage some bytes in encrypted header. (decrypt header, change and encrypt again) http://www.truecrypt.org/docs/?s=volume-format-specification byte 124 and 252
I realize this question is almost two years old, but I answer it for those who find this in search and need the answer.
First, mount your Windows partition as read-only. If your Windows partition is the first partition on your first hard drive add this to the file /etc/fstab:
/dev/sda1 /mnt/windows ntfs ro,umask=0222,defaults 0 0
You have to create a directory called windows first.
mkdir /mnt/windows
If you want to mount the partition after boot and not be logged in as root, use this:
/dev/sda1 /mnt/windows ntfs user,ro,umask=0222,defaults 0 0
To mount a specific Windows directory as read and write, use ntfs-3g or fuse-ntfs-3g. Most people will want to mount their Documents, so I will use this use example. If you are user David on Windows and david on Linux, use this (substituting fuse-ntfs-3g for ntfs-3g or whatever current kernel module you have installed):
/mnt/windows/Users/David/Documents /home/David/Documents ntfs-3g rbind,user,umask=0222,defaults 0 0
rbind is what remounts an already location to another. For a more detailed explanation of other options in the comma separated list, type info ntfs-3g in a command console. The Documents directory in Linux must exist and should be empty. This line must be after the line that mounts the Windows partition.
This is for Windows Vista and 7. If you have Windows XP, use /mnt/windows/"Documents and Settings"/David/Documents. The quotations are important because mount cannot accept spaces in the directory name even though Linux has no problems with spaces in directories.
If you don't have a kernel module that can mount NTFS as read and write, you need to install one.
Ubuntu comes with ntfs-3g, automount, and ntfsconfig. Any currently connected partition should be automatically detected and set up to be mounted automatically. Ubuntu also mounts nonnative partitions like Windows under /media instead, usually with the name of the operating system, so your Windows 7 partition is mounted at /media/Windows 7. You will find your fstab entry uses unicode strings for special characters so that the line says /media/Windows\0407, where \040 is substituted for the space without the need for quotes.
To mount David's Windows 7 documents in david's Linux home directory in Ubuntu, put this in /etc/fstab:
/media/Windows\0407/Users/David/Documents /home/David/Documents ntfs-3g rbind,nosuid,user,umask=0222 0 0
I hope this helps.
Best Answer
If you change the drive letter once, Windows should remember that.
You should also try to find out what causes the BSODs. I doubt that it's TrueCrypt alone since it runs on thousands of PCs without crashing them.
So maybe make a screenshot and post that here. We might be able to point you in the right direction.
On top of that, this blog post might help, too. Or Google for "truecrypt bsod".