F: is a Samsung Spinpoint F3 1TB that I keep my main programs/swap file/games on. My drives are set up as follows:
C: - OCZ Vertex 120GB (Windows)
D: - Optical Drive 1
E: - Optical Drive 2
F: - Samsung F3 (Main Programs)
G: - WD Caviar 2TB (Primary Storage)
Handbrake reads from one folder on F: and writes to another, also on F: normally. To see if something was up with the drive, I instead had it read the file (after copying) on C: and write to C:. There was no % useage increase even when using the SSD (C:) instead of the mechanical HDD (F:), which makes me lean toward it not being a SATA bandwidth issue.