It happens during a game, so not at the system menu when you first turn it on. and i've only been playing rpgs on the TGCD as of right now and it happens in Ys 1/2 and Cosmic Fantasy 2 at random spots.
When I hear it, it always scares me, lol even my jvc x'eye doesn't make that noise. So you would think it's the construction of the cd unit or is it wear over time (that makes the noise)