Cant find anything so far re Vista and SATA problems such as you are having
I am wondering if its a faulty cable or even drive ?
If you havent any data on it that you need or if you have backed it up already then I would try this.
Disconnect the IDE hard drives, just have the SATA connected, set the SATA drive as the first boot device and see if you can install Vista on that and see if it takes a long time to boot from that alone.
That should eliminate any probems with the SATA controller dirvers/Cables and the drive itself.
A SATA drive would be better off as the boot drive anyway, especially if running at SATA 2 speeds of 300mbps as opposed to the fastest IDE UDMA 133 at 133mbps