OK. So, on the BIOS startup, it is showing 16GB, right?
If it is, remove a single stick of RAM. Verify that it's showing 12GB total RAM on BIOS startup & in Windows. Make a note of how much usable RAM Windows shows available. Retest with each of the sticks. If you consistently get the same results, & you see both the total & usable RAM figures dropping by 4GB (matching the RAM stick you just removed), then Windows is correctly reporting total & usable RAM...it's just using a lot of RAM for whatever it's doing.
Alternately, use Windows Task Manager to see what's using your memory. On the Processes tab, click the button that says "Show processes from all users", and click the column heading labeled "Memory". This will sort all processes by order of the RAM they're using, biggest first. That'll help give you a clue as to what's taking up the memory.
The best time to do this, though, is right after booting up. That should limit any leftover applications from being in memory.