Remember that everything in your PC is memory mapped. So with a 32-bit OS it has a total of 4GB to work with. All the little controllers on the motherboard, registers of your drives, PCI/PCIe cards including graphics, etc... all get placed in that 4GB address space. So to compile for large FPGAs you need a substantial amount of memory and a 64-bit OS (and 64-bit processor) to make sure it's addressable.
You are probably on the hairy edge of running out of addressable memory when the compile does complete. For a Stratix V design you are going nowhere using a 32-bit OS in my opinion.