How should I go about investigating seemingly high disk usage?
From time to time the whole system crashes too - I think the high HDD reads/writes might be to blame.
Thanks
You might want to too look at the disk utility and take a look at the SMART Data, this gives you a good overall view of how healthy your disk is/isn't.
You can monitor what programs are causing how much IO by running iotop
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Did you skip creating a swap partition when you installed Ubuntu? If you did, add a new swap partition.
In GParted Format a partition as "linux-swap" and then right click swapon.
I had the same problem too, and this helped me.