BooBooBunny - Gravehearted gave some good advice and it's true that if a bunny is having health issues sometimes they'll go next to their box.
Here are some suggestions too: It can take weeks to train a bunny and it can take only a few days of bad habits to ruin it all. So you have to be persistent in getting good habits back on track.
1. Change back to other box that he used to use more.
2. Put hay and treats far enough in the box where he'd actually have to get into it to eat them. If he can still get to the farthest corner of the box while staying outside of it, then the box may be to small.
3. If he runs and hides while you are trying to correct him, be sure to still get him in the litterbox, otherwise he'll just end up associating pooping and peeing with being chased only which may only have adverse affects, so it's important that when you catch him in the act that you get him to the litterbox, Offer a treat once he's in there (which will mean you'll have to have some in your pocket or someplace easy where he won't hear it and get out of his box to come get it. As soon as he gets his treat, immediately give him space so he feels safe in there, like you'd leave him alone. (If he's really nervous when he's been forced to go in there, you might not be able to give him a treat, you might have to back away right away. He'll need to associate the litterbox as his safe haven.
4. When you are getting him to the litterbox, actually say the word litterbox over and over. I know this sounds crazy, but I can tell you that my bunnies understand that word now, and if they even look like they are going in the wrong place, I can just say the word a few times and they actually go to the litterbox. It took about a week for them to associate the word with the box.
Bunnies are all different, and so sometimes what works for one bunny will not work for others keep us updated. But remember, be persistent with one method for a couple of weeks before giving up and trying another.