you just have to use some common sense. You can plug in the drive no problem it will take a few seconds and it will be detected and accessible. When you want to remove it make sure all explorer windows viewing that drive are closed and that there are no open files in any programs from that drive, then go to device manager and find that drive under disk and hit uninstall, say no to reboot, wait few seconds then unplug the drive. Oh also if it's xp you can change the policy on the drive from performance to quick remove
plug in the drive, wait few seconds
go to device manager, expand the disk drives category and hit the "Scan for hardware changes" button. That works on my box at work.
On my vista box at home I don't need to do that, vista detects the drive about 10 sec after i plug it in.
It does recognize the drive, but the partition is marked as invalid, when I reboot, the partition is back to normal. Tried with 2 hard drives same results.
Oh right forgot you need R chipset for intel matrix. The problem is in order for hot swap to work the sata drive has to use ahci but when you install intel chipset drivers it installs the sata controller in ide compatibility mode. You can fix that by installing storage matrix but like you said it only works on R chipsets. Vista does have a built in ahci driver you try using it(manually choose the driver for the sata controller)
Other then that I'm out of ideas, i have the hot swap working on few vista boxes with intel chipsets but they are all ICHxR (ranging from 7 to 9) and using intel storage matrix drivers.
I tried using SATA 2 and it only worked a couple of times, most of the tries it recognized the drive but not the partition, but using sata 3 and 4 worked every time with no problems at all.
then it's a problem with your mobo, rma it. All the ports are comming from same sata controller so they should all perform equally(unless you have them disabled in bios)