When you put them in the run do they have access to somewhere safe to hide? A rabbit without a 'bolthole' will feel very vulnerable and will not enjoy themselves, they also need water while they're out there and shade. What time do you put them out too?
My rabbits have access to a run for at least 12 hours a day (it varies in size, when I'm out a 6x3 fixed run attached to the playhouse, when I'm around a huge or 9 feet open topped run). They are out mostly in the morning (about 6.30am-8.30am) and in the evenings from about 4pm onwards.