It seems, that you're right: hd tach claimed to mesure 95 MB average read, but HD Tune measures something like this:
HD Tune: Maxtor 6Y200M0 Benchmark
Transfer Rate Minimum : 28.1 MB/sec
Transfer Rate Maximum : 55.2 MB/sec
Transfer Rate Average : 44.5 MB/sec
Access Time : 20.0 ms
Burst Rate : 102.2 MB/sec
CPU Usage : 4.0%
It also shows NCQ greyed out for this drive.
So, I think the mainboard or the harddrive doesn't support NCQ.
$ cat /sys/block/sda/device/queue_depth
0 means disabled, then 1 might say, that it's not implemented?
During benchmarks there may running several processes in the background, but yacy is disabled.
I saw some benchmarks with 75 MB/sec on the net, and thought, that I should reach such throughput (==Transfer Rate Average?) under kernel 2.6.20 .
The Transfer Rate Average is 15 MB/sec higher than on linux though...