The 2+4 GB memory modules is standard VMWare ESXi practice, it maps the virtual RAM to it's nearest physical equivalent, so a 3 Gb machine has 2+1, a 6 Gb machine has 4+2, a 12 Gb machine as 8+4 and so on.
The 3 Gb value can be the result of having a 32-bit OS installed (although I seem to recall that VMWware gives about 3.75 Gb to the OS, not just 3 Gb), or having an limitation on the available RAM in the OS, check the GRUB config files for memory limits, something like "mem=3072m" or "mem=3g" on the kernel line...
I've stumbled across one of those errors a couple of months ago, this particular Windows 7 64-bit machine was reporting 1 Gb RAM, and the helpdesk insisted that they had 4 Gb there, someone had messed around with the boot options and had placed a 1 Gb RAM limit there...