What you're hearing are the switching voltage regulators working hard to keep the GPUs power supply stable. Everytime you send a command to the GPU it's power requirements increase. Using immediate mode the duty cycle between high demand and low demand is low, so the short impulses of power can be satisfied by the decoupling and filter capacitors. Display lists keep the power requirement up so that the voltage regulators have to switch up, then keep a "steady" high power output until the list is done.
Now when you are rendering VBOs and you can hear the regulators working, this means that you use about 50% of the GPUs capabilities and the regulators are constantly varying between power requirements. Your best course of action would be to increase the number of primitives processed with a single glDraw… call. Right now the GPUs finishes drawing before the next glDraw… comes in, so you're sort of starving it.