Comment 7 for bug 701753

Update

The Transmission problem may have been caused by my WD HDD.
Apparently WD screwed up the firmware.
Some of the symptoms seem similar to my problem.

Here are some links about the WD problem:

WD Caviar Green HDDs Suffer from a Critical Design Flaw
http://news.softpedia.com/news/WD-Caviar-Green-HDDs-Suffer-From-a-Critical-Design-Flaw-196159.shtml

Critical Design Flaw Found in WD Caviar Green HDDs
http://www.ngohq.com/news/19805-critical-design-flaw-found-in-wd-caviar-green-hdds.html

This problem could be responsible for this (compare with my previous post):
WD 1.5 TB internal HDD (NTFS format) - rated 71% due to Spinup time.