HDD stuck in clag, seems to pass tests (or at least, not fail them)

Question

About 12 months ago, my PB had a new HDD installed because of failure to boot with the old one. It ran fine for ~10 months, then a couple of months ago it had an episode of problems, where it ran unbelievably slowly (say 20 mins to get to the login screen, another 5 to got the login prompt, etc). But it would run OK once it had apps in memory. Seemed a very clear HDD problem again. But at that time, I had some time critical stuff to do, so I hacked my way through it as I couldn't afford the five days repairs take here. After about three days, it suddenly recovered (in the meantime, we had bought a new MacBook as backup - my wife's using it now). When I finally got to the point where I could afford to risk a full failure, and ran techtools pro on it, nothing showed - esp., no recorded SMART errors. So I decided to wait till the end of term before I took it off to the repairers. Well, that's Thursday. But in the meantime, the gremlins have reappeared. It's pretty clearly disk-related - and pretty clearly low level, because when I do an <option> reboot, it takes forever to bring up the icon of the built-in HD. However it seems a little strange, because sometimes when I do an <option> reboot, it fails to find the attached firewire drives - but when I start it again, it finds them. So that makes it look like something might be injecting noise onto the bus - except that, when I do manage to boot from one or other of the firewire drives, it runs beautifully, at normal speed.
Of course, I have also tried to check it with techtools pro. But it shows no errors - though it did hang once in the middle of the disk controller test (but stopping it and re-running it gave a green light). However I had to abort the surface scan, it clearly wasn't going to finish within my lifetime.
What happens when it starts to give problems, is I can hear it doing endlessly repeated seeks, but it eventually seems to get to read the block and goes on to the next. Then every now and then it will give a faint (and I do mean faint) squeak. It actually sounds more mechanical than electronic, though hard to be sure. So presumably something is detecting that there was some sort of hardware error. So why don't I see hard controller errors, seek errors or SMART errors in the techtools logs? Any ideas what could be the problem?
I should add that the machine has about two months of its applecare warranty left. If possible, I don't want to get (say) the HDD replaced, only to find one week after the end of warranty that it was really a motherboard problem and I'm left with a pretty paperweight... Any help in getting the right diagnosis on this would be greatly appreciated.

Answer 1

Well the local apple guys were very fast, my wife picked the machine up Wednesday morning, though I was a bit suspicious - I got her to boot it while I talked her through it on the phone, while she was still in the shop. It booted, but veeerrry slowly. The shop guys claimed it was normal.... When it came home and I tried to re-install my backups, it failed with hard errors. I then ran techtools on the new disk, this time it showed hard read/write/seek errors (I probably should have checked whether it was really a new drive, or whether they just reformatted). Anyway, with the printouts from techtools, there wasn't any argument about replacing the disk this time (and it's definitely new - hitachi rather than toshiba). This time, reinstallation wasn't too bad, and I'm writing this from the machine now. It still seems a little slow, but maybe that's because in the interim I've been using my wife's macbook...
Thanks for all your help. I still don't understand why none of this showed up in SMART status, but I guess I don't know enough about that.