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I have heard of ATA100 controllers making the time to start up drag on and on.
The CUSL2 motherboard isn't using the Promise ATA100 controller. So this may account for the difference in start up time.
"...but you could just add a device to the IDE chain that isn't ATA100 ready - which forces ATA/66 or 33 (the port runs at the speed of the slowest device." This is no longer true and hasn't been for a while. Each device runs at its specified speed without slowing the other one down.
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