Assuming that you have the D945GCLF2 motherboard and it has the same 945GC chipset and the Atom 330 Dual Core Processor, you are quite lucky of getting 3.3GB of memory available in BIOS as well as in the operating system.
This combination of chipset and processor has support for only upto a maximum of 2GB memory support. Link: http://support.intel.com/support/motherboards/desktop/d945gclf2/sb/CS-029532.htm . Hence the answer is simple, this (chipset and cpu) supports only a maximum of 2GB of memory. If you are getting 3.3GB while you are having 4GB installed, if I were you I would not complain.
I have checked it in everest, it shows me, the max of memory support of MCH is 2G, maybe it's really limit of MCH, but , how to used 3.3G of memory? are there any other way to use the full of 4G? such as RamDisk?