Thanks alot for all your comments guys.
I described them as jelly-like crystals to try and portray the fact that they looked like crystals (small and squarish) but were soft like jelly.
Well here's the verdict:
The dark, weird opening on one side of the urethra was just a build-up of something. Common in rabbits etc. Cause is unknown apparently, but it appears to be some sort of product from the sexual organs, a bit like earwax for us. It was on both sides, and he showed me- I could not hold Pippin and look well at the same time, but he held him well and showed me. He wiped it out with a wet towell and it was just like dark earwax. So that was all fine!!
As for the jelly-like urine- I brought a sample for him. I had looked up lots about it and just couldn't find something that fitted. It wasn't sandy etc. or like toothpaste, so it wasn't bladder stones etc.
But he was baffled. All the vets were. He asked whether (however silly this question) if I knew for certain it was from his urine. I could only assume so.
But he said, as it is, and in Pippin's healthy condition, and that there has been no other change, and it is not a sign of something bad, he said it is probably just fine. He said to keep a good eye on Pippin for any signs of change, and check his urine for it. If it occurs more then they will run a series of tests.
Yeah....Pippin has just never taken to litter training. It's really weird. He treats his 'bedroom' as a litter tray. He doesn't wee anywhere else in the house or hutch. He just wees in all four corners of his 'bedroom' bless him. That is not a sign of an infection etc is it? He just didn't litter train well, and has chosen four spots in which to alternate his toiletry habits lol! Both wees and poos!!
Thanks a lot guys. I am so glad everything is okay. Seeing the black swellings (I saw the black through thin skin, so it looked like blood under skin) was just terrifying. I'll keep a good eye on his urine for more jelly stuff, IF it was actually from his urine. But I can't see what else it could be from. But the vet had never seen anything like it.
He is binkying, washing, eating, drinking, energetic and completely himself, well-formed droppings and the same amount of urine as normal, with normal consistently and colour, except about 12 little tiny crystal (looking!) jelly things.