Alright. Well since you don't know what food they were on before, I'll just make a guess that it has to do with the protein in the pellets and the source of that protein. This is what I have learned about pellets and protein. Excess protein in the urine makes the urine STINK like ammonia. The source of the protein also makes a difference, and I learned this trying to switch my rabbits pellets. For the past year I had been feeding Sherwood forest pellets. The protein level is pretty high, I think 18%, and the protein comes from alfalfa hay, but my rabbits pee didn't stink like ammonia, and I have 11 rabbits indoors, so this makes a big difference in odor control. At one point several months ago, I decided trying to switch to a different rabbit food that had 16% protein, but it had soy meal as one of the sources of its protein. I didn't get even halfway through trying to switch before my rabbits room started stinking like ammonia. So I decided to keep them on the Sherwood food. As soon as they were switched back and off of the rabbit food with soy, the ammonia smell stopped. I now have them on a different rabbit food that doesn't have soy meal in it, and same thing as the Sherwood, no strong ammonia smell. Most rabbit foods have soy meal in them, but the problem with soy is that part of the protein can't be utilized and so is excreted in the urine, creating that annoying ammonia smell.
It's possible that your previous rabbit food didn't have soy meal in it or not as much as your current rabbit food, so you are now noticing the increased smell. Aside from changing pellets, it may help some if you have a thick layer of wood pellets so that the pee drains to the bottom and is covered up by the pellets and sawdust, so that it helps trap the smell better. You may have to change more often too, at least the wet part. When I had tried to switch my buns pellets and they started to stink, I was having to clean out litter boxes every day.
The other alternative is switching pellets to something with no soy or a lower amount. Maybe you got the ifa bag with 20%, and that could be one good reason for the stronger smell. If you still have your receipt it probably has which type of feed it is that you bought. You could try a lower protein pellet or try calling the shelter and asking what kind of pellets they use.
Aren't your buns angoras? Do they need a higher protein pellet?