It may be the following...
The 2006 owners manual, page 336 states the following,
"You may hear a click or motor sound in the engine compartment for a few seconds when the engine is started of just after the vehicle begins to move. This means that the anti-lock brake system is in the self-check mode, and does not indicate a malfunction"
Our Highlander does the same thing, so did my Subaru's before that.