shelleycat
The brown color is partially bile, but mostly bilirubin, which is released with the bile. Bilirubin is created by the liver as it breaks down old red blood cells, thus the dark color.
A tan or clay color indicates that you've eaten too much fat or that there wasn't enough bile to digest the fat (liver depleted by flush). So you're absolutely right, you're probably not producing enough bile.
Try eating a low-fat diet, with no hidden fats, such as in breads and desserts, no dairy, for awhile to give your liver a break. Then see about taking herbs to increase bile flow, such as Coptis from www.sensiblehealth.com. Chinese Bitters would be helpful too.
And keep drinking apple juice and eating green apples! the stones may be shifting and blocking ducts temporarily. Are you experiencing any gb pain?