With 3GB or more, programs just get screwed up reading it. Same thing happens on my 3GB 7970. It doesn't mean anything other than programs aren't really designed to read vram correctly in such large amounts.
Windows is adding the graphics + system shared memory to get the "total memory". It's also an ignorable number.
This... you're putting yourself through undue hardship by fretting over it. Don't... trust me, it's fine. You'll never touch that shared system memory since the 680 has plenty of VRAM. The shared memory just addressed in case you ever needed it (which you won't).