Rabbits are prey creatures and very prone to anxiety. This anxiety can lead to heart attacks, so try to minimalise it.
Laying down and coming to you for pettings are great signs, and maybe you should try and keep him in that room for a while to give him some recuperation time. Rabbits are extremely sensitive, and certain sounds and smells can be too extreme to them. Observe the rabbit closely and try to figure out his stressors. Learn about their body language here: http://language.rabbitspeak.com/

There are many things that may upset a rabbit, but these are the most common ones:

– Noises, especially noisy kids, TV sounds or music. My rabbit gets agressive from the high frequency noises of electronics on stand-by, such as monitors and phone chargers. Rabbits’ ears and feet are insanely sensitive. They react strongly to high frenquencies and low rumbles.

– Smells: my rabbit gets frightened when I bake meat or anything which gives off a slight smoke. He hides in his box and won’t come out until the smoke has gone again.

– Other pets indoors or cats in the garden. They can feel hunted if other animals are close.
– No place to hide in. Rabbits in the wild have burrows where they hide in, domestic rabbits still have the same instincts. Giving them an upside-down box with two entrance holes can calm them down immensely.
– Not having firm footing underground. Rabbits like to be able to run away at any time. Picking them up or restraining their movement can frighten them. Keep a bit of distance while petting him, that will help strengthen the bond between you. Trying to calm him down may have the opposite effect.

Hopefully you’ll find out what’s bothering him soon