Cat has strong ammonia urine and high lipid level in blood?

I took my cat into the vet because his urine was smelling like ammonia. I decided to go ahead and do blood work and a urinalysis to get everything checked. He can't have vaccines as his body can't handle the antibodies and he gets incredibly sick, but he is inside only. He came from a feral colony and I got him when we was about 4 weeks old. He has some other issues----his lower spine is partially fused and so are his hips so he walks awkwardly and isn't very graceful. He is not in any pain from this it's just like a birth defect thing. Anyway, on to the point. His blood had such a high lipid level that the machine at the clinic couldn't read it and they have to send it off to get processed and see what's going on. They said not to worry, but my cat isn't overweight and even if he were, his lipid level wouldn't be that high unless there was something going on right? Any thoughts as to what could be wrong? I am kind of freaking out waiting for the results and would just like to somewhat prepare myself for what could be wrong.