Ubuntu 9.10 installer doesn’t recognize the hard drive

I assume from the size of the drive you are talking about, that you are either using a relatively expensive SSD or a spinning-disk based drive (rather than a "pen drive" or similar).

If using a spinning-disk based drive then you might find that the problem is due to the controller in the drive's enclosure not appearing to the BIOS as a bootable USB device until such time as the drive has fully spun up. Depending on how long the drive does take to spin up and how long the BIOS to do the rest of its POST. The POST will be shorter then when starting from a power-off state (usually no RAM test and so forth) for a warm boot so the drive has less time to be ready before it is scanned. This would explain you having more luck when power cycling the machine.

Some BIOSes have an option to pause for a few seconds before scanning for drives, to account for this possibility. If yours doesn't (it is less common now than it used to be) then you might have an option to force a full POST even on warm boot.

I'm adding a new hard drive, a Seagate ST31000340NS. Interestingly, the bios recognizes it as a ST31000340AS, but it was bought as the other number...

If it were me, I would take the sucker out and check the label to make sure it matches what you bought. And if after you get past your current problems if the drive model is still reported as AS rather than NS I would check with Seagate about it.

The ST31000340NS looks to be the enterprise version of the drive and I assume you paid a premium for it. Seagate may indeed sell exactly the same hardware and only change the labels and the warranty periods ... but you should at least get the label you (I assume) paid extra for. No?

Finally figured out that the hard drive needed a jumper set to limit the speed to 1.5gbps so the mobo would recognize it, and the bios DOES recognize it now.

This is supposed to be auto-negotiated ... oh, well. Suppose it doesn't make any difference since the board apparently doesn't support anything better than first generation SATA speeds.

But not windows (using windows 7), using add new hardware or diskmgmt.msc.

"Add new hardware" is not where I would be looking. I would look in the device manager (run the command devmgmt.msc in a command prompt). I expect you will find the drive listed there. My guess is that it is probably also showing up in diskmgmt.msc and just needs to be (1) initialized (assigned a MS serial number?) and (2) formatted. But WTHDIRK?

Ubuntu livecd recognized the drive

Which is why I expect Windows 7 will also recognize it. I seriously do not see how this could be a driver issue. Any drivers for the chipsets on this motherboard would already be included in Windows 7.

You might have a problem with Windows XP if you used too early a version. Heck, the early versions of Windows XP did not even support a hard drive capacity larger than 128GB. XP was around a long time and went through some changes. But so long as you were using at least XP SP2 you should have been OK there as well.

The only other info I can think of that might be immediately relevant is that the drive is plugged into the fifth sata channel, and the first channel is empty. Is this a problem?

You lost me here. Below is an image of the motherboard from the link in your question. There are only four SATA ports on this board. Why are you talking about the "fifth sata channel"? There are only four SATA ports unless the motherboard reference you gave is wrong.

Are you using the latest BIOS? If not I would get it from HP and upgrade. (It was dated Dec of 2007 IIRC).