Ok, i just had this problem actually. I have had 3-4 Kidney Stones in the last 3 months.
Doc and specialist says its not the protein. For me my body wasnt liking the creatine i was taking for one. It elevated my creaktine CPK (spelling) levels serverly which ended up dehydrating my kidneys too. I have been urinated some blood off and on from the start of it.
For me it was later found out it had to do a lot with my genetics. Father had a bunch around this time when he was my age.
But from the doc's ive seen they said no protein doesnt effect the kidneys.....liver on the other hand though.