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*spalko*
I feel like you are the animal whisperer around here 
I need help!
I am so extremely frustrated with our cat Henry...
We have him and Nala the calico, we got Nala first, then 9 months we got Henry. Henry was a stray and he never covers his poop in the litter box, well maybe sometimes, but most of the time, no.
Our litter box is in the basement and we just leave the door open. In July we had a water leak that caused some flooding in the basement and Henry pooped on the floor. I know it was his because his poop has this horrendous smell compared to Nala's.
DH and I thought it was just a fluke, but then after the basement was all cleaned up he did it again... about 5 feet from the litter box, and it was empty! We are really good about cleaning the litter box before and after work and then again before bed. Plus I empty the whole thing and clean the pan every few months.
Another time he pooped in the basement and then he did it a few times in the living room.
We recently put in a cat door to the basement and he has pooped outside the litterbox twice more in the living room!
The crazy thing is, is that he still uses the litterbox, he is able to use the cat door to the basement. I don't know what is going on!
Please help
Re: *spalko*
When cats become stressed they typically show it to you with bowel movements or peeing on things. Anything can stress a cat out, and I mean anything! My guess is that all of the stress with the basement was enough to set him off and now it has become a routine for him. We usually recommend that people have enough litter pans for each cat plus one extra so in your case you would need three total and they don't have to be scattered all around the house either. Maybe try putting another pan in the basement along with the one that is currently there and see if that helps any. We have some cats that live in the clinic and they will use one pan to poop in and another pan to pee in, cats are just weird.
With the pooping in the living room, where is he doing it in relation to the litter pan? Is it right next to it or in another corner of the room? If it is away from the litter pan, try moving the current pan to where the poop tends to be at and see if he starts using it then. If he does, slowly move the pan to where you want it to be - when I say slowly I mean like every 3-4 days move it a foot (again, cats hate change!) so he can get used to it before things are changed again.
He's not in pain or anything when he goes to the bathroom is he? He's not straining or anything when he poops? Is it always #2 outside the pan or do you ever find pee around the house? Another reason for his sudden strange behavior could be that something happened to him when he was using the litter pan, either it hurt really bad when he tried going or something scared him enough that now he associates that pain or feelings of being scared with the litter pan. Maybe watch him a few times when he goes potty (weird I know but the things we do for our pets) and see if he appears to be in any sort of pain or if he is straining really hard to get the poop out. If that is the case, he needs to be seen by a vet to figure out what the straining is caused by. Are his poops really firm or more like soft serve ice cream? He may be experiencing some constipation (or had at one point while using the pan). So watch him for awhile and see what his bowel movements are like and go from there.
As far as the not covering is poop, well if he was a stray he probably never did it in the wild because it would let other cats know that he had been there. It's a marking mechanism for cats so he's telling your other cat that this is his pan!
Keep an eye on him for awhile and let me know what you find out. See if adding another pan will help him be more comfortable with using it. Also, is there food close to where the pan is? Some cats won't want to poop or pee if their food is close by.
I hope some of this helps, if you need anything else just let me know!
Thank you so so much for your detailed response, both DH and I really really appreciate it! Too answer questions...
The living room is on the main floor of the house (1 story plus the basement). It has been only poop and it looks like soft serve ice cream haha. I have never seen him actually go but I will definitely be watching now. He seems healthy otherwise.
We keep the food in the kitchen so it is really far away from the basement.
We will try two pans in the basement and should we put one in the living room for the time being?
Thanks again!!
I'd still keep one in the living room for the time being just so you don't freak him out by completely getting rid of it. If you want you can slowly move it to another spot in the house where you would rather have it, just remember to move it slowly.
That is good that his poops are soft. Just keep an eye out for if they get really hard or runny. My guess is he is just being a butthead boy kitty and will eventually come back around!