Imzadi - how old was your cat when she was taken away from her momma? I've noticed the not-covering-poop thing seems to be related to kittens who didn't have momma kitties to teach them this bit of information.
I'm not sure if that is the problem although I got her from the pound when she was 12 weeks old. She didn't even know what kitty litter was. She played in it

until I took her paws and did the scratching motion until she caught on.
She does know how to cover. But, she
will only cover her poo if the litter is brand spanking new & freshly poured. Then she's digging in the box for several minutes, covering nicely. So she does know
how. But, once the litter is used
twice, she will never cover again,

even if I scoop & pour in fresh litter on top & mix it in.
I guess I can't blame her, I wouldn't want to dip my paw into urine soaked litter, even if it had been scooped out. I just cant afford to be dumping all the litter after two uses.

I tried both putting in inches of litter so she'd have enormous amounts to dig and cover, (didn't work,) to using as little little as possible as she won't cover, and adding on more after each use.
I did realise one thing last night.

Sometimes, she will poo, then jump out of the box and start pawing the ground
next to the box. Then she'd look back and see if the poo was covered.
Umm, no, you have to be IN the box and actually scratching the litter for it to cover. She'd always scratch some more, but didn't seem to get that correlation.

(Again, she does it fine when the litter is new.) Finally, she'd give up, and meow to tell me to cover.
Last night, I realized, I had placed the new box in the spot she'd been scratching. She did cover reasonably well last nite. Although it was new litter, too.
Maybe all this time she just needed a longer box and more space to scratch?

It only took 6 years to figure this out.

I might switch to one of those plastic, under the bed storage boxes as they are longer. But I don't think I can find white plastic trash bags long enough to use for liners. Right now, I'm using the tall kitchen bags, and they just fit enclosing each box. I don't want to go changing things up too much, so that a different problem is created and she won't use the box at all.
