I think I can shed a little light on that distinction -- here's how I understand it. No serious formal study here, but a few classes and a lot of reading of Hindu texts under my belt:

The human "Self" -- capital S -- generally refers to Atman. Atman is a "shard" of Brahman. So Self does denote Brahman, but with the tacit understanding that Atman is itself composed of Brahman, like a small patch of a flowing stream. It's not its own separate entity, but rather a piece of the whole that is also representative of the whole (look up "Tat Tvam Asi" for more on this concept).

The self -- lowercase s -- is generally used to refer to the dual self that humans have: Atman and Jiva. The Atman is the Self as we discussed before (but the Self is also the divine, as Krishna claims throughout the Gita). The Jiva, however, is the discrete part of the self -- the ego, all wants/desires, attachments to sense-objects and the physical world. When in casual conversation we discuss ourselves, a Hindu would likely claim that we are in fact discussing the Jiva.

Thanks for the explanation.

sigh This is one of the problems that comes with trying to map these traditions into our common English vernacular. We end up inventing new words (like capital Self vs lowercase self) or worse (as is often the case in buddhist circles) we borrow terminology from Freud (ego) and reuse it in ways that would have the Austrian neurologist flabbergasted.