Solved it, after reading the clue on a german forum: The 'Halt' power saving CPU state causes the harddisk's poor performance. Disable Halt with the BIOS or with CBid and the disk's transfer rate doubles. But because 'StpGnt' power saving CPU state can still be enabled the CPU seems to remain cool..

A somewhat related issue: Soundblaster Live Soundfont midi rendering gets audible interference when enabling Halt state.

HLT slowing the HDD. That's a new weirdness. Maybe an ACPI quirk with that board?

Another possible cause is problems with APIC (that's not ACPI). I had problems similar to yours with SBLive on a nForce2 mobo when APIC was enabled. APIC allows for many more IRQs than the standard PIC. Sometimes it doesn't work quite right on older boards.

StpGnt is Stop Grant. http://www.hardwaresecrets.com/article/611/3 . This is a nice feature that can cut power consumption a bunch but I've had boards that have audible VRM noise with it enabled.

I see, I will try what APIC settings are available and what they do. (but not today...)

To still enable StpGnt on this mobo, I now have to use the Coolon utility (http://coolon.o-ya.net/en/), but comment out one line in the coolons.ini file so Halt remains disabled and StpGnt gets enabled. Like this:

[Discon:11063189] ; VIA KT400/KT600
;00:00:0:D5=|02
00:00:0:D2=|80

It is odd that for years I thought everything with this system was fine, and now to discover it was partly crippled.