Tweakboy (got your PM), and I read all of this. I'm still not clear on which of the HD's is your main drive. You really can't compare one to the other unless both are just blank drives with no OS on them, or both need to be the boot drive (which isn't going to happen). I can only speak for XP, but when I did all of my benchmarks I told you about, the HD's tested were blank.
Or, the boot drive could be partitioned and you could test the blank partition. I have done that with the same results as the drive being bare.
Both HD's also must be on the same controller type; either Native or 3rd-party. I get totally different results comparing the Native Intel (or AMD) controller to that of a Promise (or JBMicron) 3rd-party controller. In my cases, the Native controller usually gives much higher
average rates, where the Promise gives much higher
maximum and buffered rates while having lower avg rates.
Those spikes in the HDTune graph could indicate two things: either the HD is defective, or there's something running in the background. Since you said the results are totally different in safe-mode (and better), that would point to the latter. Before any tests are done (as another mentioned), you need to
be sure nothing is running in the background. No AV software, no anti-malware software, no print spooler, Image Acquisition, BITS, Auto updates, etc., etc., all of those Services need to be shut down, and the System Tray empty, and any screensaver or monitor-power-down disabled. (And again I don't know if Win7 even has these Services as XP does). But the bottom line is the same and that is only essential Services to the functioning of the OS should be running. CPU usage should be zero before any tests are run.
But if both HD's
are on the same controller, and
both are bare, and both cables are the same, new, and working perfectly, then something is wrong because the spikey characteristics of the 322GJ should also be shown on the other HD's tests.
The 322GJ also has a 16mb buffer like the WD3200AAKS, I don't know if the WD drive is 1 or 2 platters, but we know the 322GJ is one (halved 667gb) platter so even if the WD is 1 platter it still has much less areal density than that of the 322GJ. So according to those facts, the 322GJ 'should' be faster, and at least according PassMark benchmarks, the 322GJ is MUCH faster:
http://www.harddrivebenchmark.net/high_end_drives.html
There's also the possibility the 322GJ has some kind of firmware that might require either updated/different drivers than you are using in order for it to see its full potential, or even a different controller type, or the firmware could just be flaky period.
So be sure of those things I mentioned above, be sure those circumstances for testing both drives
are identical in every way, then post back what happens after testing again.