Large Drives and USB Enclosures

OK, this is definitely a talk to the rubber ducky kind of post.

I have an old Mandrake box that various clients send their backups to overnight. I hook up an external USB drive and run a script that basically rsyncs the various backups to the external drive to be taken off-site. Been doing it this way for a while now.

I've upgraded the size of the drive in the external enclosure a couple of times, 160G to 320G to 1TB recently. When I first got the 1TB enclosure, I partitioned it with an iMac, then remembered I couldn't format ext3 with the Mac, so I connected it to a linux box and formatted it, but left the partitioning alone. Turns out the iMac partitioned it GPT. I only realized this after I'd been using it for a couple of days. This is in the logs.
kernel: /dev/scsi/host39/bus0/target0/lun0:<4> Warning: Disk has a valid GPT signature but invalid PMBR.
kernel: Assuming this disk is *not* a GPT disk anymore.

It was working, I didn't have a handy spot to move the large amount of data on the disk to, and fixing it seemed like it would probably destroy data, so I left it for a bit. I tested restoring data from the drive to be sure, and everything was working fine.

A couple of weeks later, during a really busy spell, I noticed the daily rsync jobs turned deadly slow. Instead of 6MB/s I'm getting 300k or less. Almost like it was swapping to USB1.1 instead of 2.

I twiddled with it for a bit, and since it was somewhat intermittent I tried replacing the USB controller (it's an add on card) in the server. Over the next couple of days I tried another USB enclosure, another USB cable, and copying files from different server. The problem kind of came and went, so no one change seemed to be the fix.

Since this is the off-site backup, I had started using another (smaller) drive to copy the recent information to - this setup was working fine. I bought another 1TB drive and enclosure, both different brands than the existing units, partitioned and formatted it correctly from a linux box, and started using it. It was running fine at full speed. When I had time I started copying the older archive info that was only on the first TB drive over as well.

Now this morning that new drive started running slow....

The only thing that makes any sense at all to be at this point is some problem with USB enclosures and large drives - e.g. once it gets past 650meg or so they start having problems? But the two enclosures are completely different chipsets - one has IDE + SATA, the other is SATA only. It can't be that widespread an issue can it?

OK, so now I've typed all this out, the ducky still hasn't said anything...

Anybody else want to comment?