This sounds like a food sensitivity (possible allergy). The medicine and prune juice will only deal with the symptoms (constipation) they won't solve the problem and aren't meant to be used as a long term remedy.
First off are you taking any vitamin/mineral supplements. Iron supplements & iron fortified foods often cause constipation in infants (and adults). (Beware baby foods are highly fortified, so take care when introducing them OR avoid baby food altogether and start with table food :D) Take a break from your supplements/fortified foods and see if you see an improvement. If your supplements are the culprit, I've heard that "Floradix" has and iron supplement that does not cause constipation and is much more readily used by your body.
If there's no improvement within a week try eliminating any food categories that you consume on a daily basis (dairy, wheat, gluten, eggs, soy, corn are the biggest offenders in the standard American diet and they're hidden EVERYWHERE, but if you eat bananas or rice every day then those are just as suspect). Once the constipation subsides, try introducing the foods categories one at a time at least 3 days apart if there's no reaction. If there is a reaction remove the food again and wait until you return to a non-reactive state.
Start a food diary. Record everything you consume (include brand names where applicable and don't forget to note things like your vitamins and medications). Note any changes in your daughter's eliminations and mood as well as any other significant changes (sleep patterns, skin conditions, fussiness, etc). This will help you pinpoint your daughter's sensitivities much faster.
A RAST allergy test might be worth doing, but it will probably not tell you what is causing your daughter's constipation, because they only test for IgE reactions which are immune system reactions, not gut reactions, so even though it's tough the elimination addition testing method will give you the quickest and clearest results.
Hope you find something helpful in that novel :D