heya,
Im in the same boat. Just my HD is 250G.
The solution most likely is a ext2/3 driver for windows. There are a couple floating around, and they are pretty stable, I heard.
I have like 8K titles in my library, and have the same problems.
Whats worse, other tasks get suspended during a media-scan, and the slug generally behaves unstable with ongoing NTFS I/O activity.
I dont know if tools like partitionmagic or acronis diskdirector are capable of converting NTFS to ext2, which would rock.