My cat won't use the litter box unless I am in the same room

A little background: I have a 3 and a half year old Russian blue rescue named Sterling. Within the last couple months, Sterling was diagnosed with urine crystals and started a new diet of urinary care food (Hills Prescription Diet c/d Feline Multicare with Chicken Urinary Care Health Dry Food). So far, this has never caused him to go to the bathroom outside of his litter box. He has an open top box in a non-busy corner of my bedroom and is the only animal in the home. It is located away from his food and water. 

I have noticed recently that, after I get home from work, he will cry and bat at my legs until I walk into the room and stay there for a few minutes before he will actually use his box, and his pee stream will usually last upwards of 20-30 seconds. I cleaned his box in the morning and there was nothing in there when I got home from work that night. This is leading me to believe he wont use his litter box until I am in the room, and with his condition, that makes me really worried. 

Right now, my friend is able to go over in the afternoon and see if he'll pee, but we won't be able to do that forever. Any help or advice would be appreciated! 

When a cat is outside the time when they are "going" is a vulnerable one. You will often see cats who go outside watching other cats or humans they know for hints that there is danger around them. It could be that your boy is reverting to instinct because of his recent problems. He is scared to go because it was hurting and has tied your presence to it being "safe" to go.  

If I am right, there really isn't much you can do except wait for him to realize he doesn't need you watching for him to be safe. You could try Feliway which gives off a pheromone that can help some cats feel safer. I am one of the people who didn't actually have success with Feliway but there are people who have so it doesn't hurt to try.