Place cream cheese and 2 tablespoons butter in bowl of electric stand mixer. Attach flat beater to mixer. Turn to medium and beat about 1 minute. Stop and scrape bowl. Add 3/4 cup flour. Turn to low and mix about 1 minute, or until well blended.
Form mixture into ball. Wrap in waxed paper and chill 1 hour. Clean mixer bowl and beater.
Divide chilled dough into 24 pieces. Press each piece into miniature muffin cup (greased, if desired).
Meanwhile, melt remaining 1 tablespoon butter in 10-inch skillet over medium heat.
Add mushrooms and onions. Cook and stir until tender. Remove from heat. Cool slightly.
Place egg, remaining 1 teaspoon flour and thyme in mixer bowl. Turn to medium-high and beat about 30 seconds. Stir in cheese and cooled mushroom mixture.
Spoon into pastry-lined muffin cups. Bake at 375 degrees for 15-20 minutes, or until egg mixture is puffed and golden brown. Serve warm.