litter box anxiety

Hey everyone!
So I recently adopted two cats that lived in a cattery for long time where they shared one litter box. There were no issues with it then. Now, they have three and Minnie seems like she's a little anxious about using them. There's one in our bathroom, our bedroom where they sleep, and the living room, which goes unused. Occasionally we'll see our other cat Big chase her when she's excavating in a box, which I'm thinking is what is causing the problems. She typically will pee in her box no problem but will hold her poop all day till everyone goes to bed, then she'll go a couple of times but often will go right next to the box. She's always had issues with pudding poop so I'm not sure if it's her not feeling well. After several trips to the vet they found tritrichomonas and coronavirus, so she's on metronidazole, probiotics, some immune boosters, and royal canin gastro dry.
I'm pretty sure it's our other cat that has her a little freaked out. When I'm getting ready for bed, I'll take her into the bathroom with me and let her do her thing while I'm brushing my teeth and stuff. When the door is closed she usually goes right to the litter box and poops but just a little.
Anybody have similar issues or advice?

Oh and I clean the boxes twice a day and bleach and refill with litter maybe every other week.

Don't really have much useful advice but the word Bleach jumped out at me: maybe she is particularly sensitive to that smell?
OTOH, some cats *like* the smell of bleach.
If there is a litter box she always avoid, perhaps getting a new one (you can get them cheap at the hardware store--look for a paint type of tray).
But it could also be she associates messy, smelly stool and discomfort with the litter box.
And yes the other cat doesn't help...
Finally, there are several articles that might help you. Here is one about location http://www.thecatsite.com/a/litter-box-location-secrets and others are here http://www.thecatsite.com/atype/45/Cat_Care

Good luck!

Thank you for the response! I didn't consider the bleach. I just read that tritrichomonas can be persistent so I try to keep the box relatively clean. I'll try another type of cleaner.

Try natures miracle, cheaper on Amazon.