In my question above, I stated that the BIOS saw the 6GB. I said this because when booting, as it showed the device info etc before booting, it listed 6GB of RAM.

John suggested I look for a setting for HPET and in doing so, I discovered that the BIOS Setup was reporting that the only usable amount of System Memory was something like 4.3GB.

This obviously shows it wasn't a Ubuntu problem (wish I'd found this sooner!) and replaceing one of the 2GB sticks for 2x 1GB sticks gives me the 6GB I was looking for.

My memory config before was:

DIMM0: 2GB DDR2

DIMM1: 2GB DDR2

DIMM2: 2GB DDR2

DIMM3: EMPTY

My configuration now is:

DIMM0: 2GB DDR2

DIMM1: 1GB DDR2

DIMM2: 2GB DDR2

DIMM3: 1GB DDR2

This only came about because I had to remove a faulty stick! But at least it's sorted now!