Hi.
I am having the same problem, what was that, that you actually did to improve the performance with that hard disk, I think I have the same hard disk as you.
I captured the video using the PAL anamorphic 25fps, then created a sequence with this setup:
Frame size 720 x 576 Aspect Ratio CCIR 601 / DV PAL (5:4)
Pixel aspect ratio: PAL CCIR 601 (720×576)
Field Dominance: None
Edit timebase: 25
Quicktime Compresor: MPEG-4 Video
then I exported using the a quicktime conversion H.26.4, frame Rate current (25fps), keyframes (automatic), compressor quality high, Encoding Best quality (multi-pass), data rate optimized for CD/DVD-ROM.
Do you know what is wrong?