I have a 2006 es330 and have had a similar experience. When the engine is running and I push the trunk release button on key fob, the trunk will NOT open, also won't open on trunk release button on dash (with engine running). But if I shut off the engine both will work.
When shopping with the wife, and she goes back to the car early and runs the engine for the AC, and when I finish shopping and come back to the car and press the trunk release on key fob, that is when I have the problem. Really don't know if that is programmed in the computer or not, but if it is it needs to be changed.
Worth a try before a trip to the dealer.
Oh - by the way - I LOVE my lexus!