I have several old Xeon Server that boot an 32bit Ubuntu Desktop over Lan. These work fine.

I have just bought an AMD FX8350 with 32Gb which I have booted of the same setup. However anything involving disk access is horrendously slow. i.e. doing an "apt-get update" is horrendously slow when it gets to reading the database.

Can anybody give me any pointers to try an diagnose what is slow and how to fix it?

I found for large (>= 1.5TB) SATA 3 and 6 drives that the old MSDOS partition is a problem. I partition and format using gparted, typically from a GNU system rescue flash drive. Set the partition to gpt. This fixed the problems I was having w/ 2TB disks. Processor is an AMD Athlon dual core AM3 w/ 16GB of RAM and a 3.4.37 PAE kernel (compiled by me). OS is Debian Squeeze and the GUI is XFCE.

I have a 2 TB sata3 drive with 4 partitions and there is no speed problem at all. Probably the size of the partition? Or the driver?
Have you checked /var/log?

Thanks guys, I was working round to it could be memory, never thought it could be hard drive size. (The network drive it is booting from is 14Tb) Although the other machines boot from the same drive, and don't show the same symptoms. Which indicates more memory size.

Anyway overnight I rigged a 64bit boot together for this machine, and this is so a whole magnitude faster. (As you would expect)

Next I'm going to try and make the home folder a link to the 32bit home folder, and hope it doesn't smash anything up. That way they should look the same, but be the relevant 32/64 bit.