Could it be colitis? It is diagnosed by colonoscopy and a biopsy. It is usually caused by IBD, but there are other contributors that might cause it. I am not very familiar with it, so it would be best to consult with a trusted vet. Also, have you thought about looking for a second opinion? I am not undermining your current vet, but sometimes it helps looking for a 2nd, 3rd opinion when it is a chronic issue and none of the prescribed solutions have worked. I have gone on for 2nd, 3rd opinions even though I loved my primary vet (when we lived in San Diego) at other respectable clinics for my GSD.
This is just food for thought, but have you thought about re-vamping Ender's diet completely?
My friend breeds working Goldens in NH and has a male that developed dire rear issues since puppyhood (~ 12 weeks) and despite multiple vet visits & trying different high quality kibble, could not calm his digestive tract. Every time he came off the bland diet and back on kibble, the cycle would start. They had fair success with California Natural, but his system would still wonk out on occasion.
Finally a friend suggested the raw diet. By then she was so desperate, she gave it a shot. It was 100% successful, even doing away with chronic ear infections & hot spots. Several months later, she converted the rest of her pack to raw as well and has been feeding that ever since. This was years ago, when I was still in college, but that story always stuck with me. The pup is still around, happy and healthy. :-)
I am not pushing for raw, but since there are similarities, that you would be interested to hear about it.
Good luck, and I hope Endar and you find a workable solution soon.
ps: Usually when my dog has runny stool, I put her on a bland diet with some pro-biotics till her system calms down. It is different for one whose dog has chronic diarrhea, but perhaps you can just do a burger & rice diet till his stool hardens up.. and slowly reintroduce the kibble.
Janka vom Grunenfeld, BH (d.o.b. 10/12/07)