Hi Endeaver, I'm not trying to stalk you! Your setup is same as mine and you are finding similar issues to me so heres my solution if you need to keep the drive as ntfs.
You need to partition the drive into 2 parts - ntfs and ext3. The ext3 portion does not have to be large. i have mine set at about 500mb on a 2tb hard drive. With this method windows recognises both partitions using samba.
I store my bin files on the ext3 portion and transmission downloads on the ntfs portion.
Windows will still recognise the ntfs portion if directly plugged into a computer.
Th free Easeus partition manager allows you to shrink your current ntfs partition without loosing your current files and create an extra ext3 partition. http://www.partition-tool.com/download.htm