Stimulant medications include both: amphetamines (e.g., Adderall) and methylphenidate (Ritalin). The later doesnt show on a standard 5-panel test. Your daughter's doctor should be well aware of this unless they slept through pharmacology!!!!
Well, I have included some links that have info. A summary would be that they should stay in system for up to 48 hours, but drinking Orange juice or similar thing will speed up the elimination (I have also read that elsewhere). But, it depends on the med. regular ritalin will be eliminated faster than the SR version. And, it is also pretty common for a child(?) to not go to the nurse for the med.
Links are: http://drug-alcohol-testing.blurtit.com/717057/how-long-does-vyvanse-stay-in-urine
http://www.livestrong.com/article/215086-what-drugs-are-tested-for-in-a-urinalysis/#ixzz2ZWZd9pkk
Apparantly, the doctor is questioning the speed at which your daughter goes through her meds? Pretty easy to keep track of what is sent to the school (call the nurse) and what you have at home. An easier answer is to switch to Concera or Vyansse and take it once in the morning where you have total control.
Any way, you look at it, you need to have a talk with the doctor. This should be able to be controlled without urine tests.