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Here is one section of the Intel website covering the matter: http://www.intel.com/support/motherboards/desktop/sb/CS-028426.htm#memorylimits
but in my experience with the DG45ID's onboard everything, having under 3 GB left after starting out with 4 GB does seem a tad low.
I'm not familiar with that board but the memory will still be being used for aspects of the systems functioning and it's not gone to waste - it's just Windows can't have it. You could try updating to the latest BIOS version for the board and that may make some improvement but the thing to remember is the memory is not being wasted.