loudmouth,
For what it's worth, that sounds like normal behavior (if this is an NTFS partition) on a notebook computer. There's a fair amount of data gathering going on for the first couple of minutes after startup, and a notebook's drive is SLOW compared to a desktop's drive. If this is a drive which was converted from FAT32 to NTFS, then you have 512 byte clusters, and that greatly exacerbates the problem.
All of the notebooks I've seen running W2K on large NTFS partitions do this.
If you want to experiment with DMA, the settings are under the primary and secondary ide channels in Device Manager. I suspect that turning DMA off would make things worse rather than better.
My guess is that you'll have to learn to live with it. I've set up dozens of desktops and notebooks in this OS. The recent desktops take about 45 seconds to a minute or slightly more to boot. The notebooks take as much as 4 or 5 minutes before all drive activity ceases, though you can usually start doing some types of work (like getting connected to the Internet) during the final couple of minutes of disk activity.
Hope you get it sorted out to suit you.
Regards,
Jim