Here is one way to explain it: today's nanotechnologies use big machines to make small products -- by contrast, molecular manufacturing will use small machines to make big products. That sounds simple, but it is really a profound distinction.
Due to scaling laws, these intricately constructed nanoscale and microscale machines will work much faster, using bottom-up, atomically precise manufacturing to build revolutionary products. This will impact nearly every industry and all areas of society, from local to national to global.
Another way to recognize the huge leap from nanoscale tech to advanced nanotech is this: today's technologies will enable conventional factories to make improved products by providing better materials with unusual properties. Molecular manufacturing, however, will not just make new products, but will provide a completely new means of production.
We're talking about factories that make factories -- each one of them could make a powerful new factory every few hours. This provides the possibility of exponential proliferation, not only of factories, of course, but of their products, both benign and dangerous.
By comparison, nanoscale technologies will provide incremental advances in materials and products while creating familiar problems (such as chemical contamination). Molecular manufacturing will lead to revolutionary advances but at the same time will create unfamiliar problems and unprecedented risks.