Have you tried different litters as well?  That's all I can think of.  He
may not like the texture or scent of the litter itself.

And yes, a couple of my cats try to cover their food, or partially eaten
food of another one of our cats by scratching the floor.  I've even seen one
of my cats do this to dry food.  Normal!  :)

so, you have more than one cat, and you have one box? and it is covered?

Some cats are particular and refuse to both poop and pee in one box.  The
experts recommend 1.5 litter boxes per cat, so if you have two cats, three
boxes wouldn't be out of the norm.  There is a litter out there called Cat
Attract that is designed to attract your cat to the litter.

Since it sounds like your litterbox is covered, uncover it.  Most cats don't
like to be crowded when they use the facilities.  Consider where you put the
box.  Is it a high traffic area?  Might he not feel comfortable using it due
to lots of noise?

Not covering poop is usually  a sign of dominance.  Trying to state that he
is the alpha cat.  it is also a sign of old age, and no longer being
bothered to care who is the alpha cat.  My elderly arthritic cat hates going
IN the box, she likes to go outside of it, so I simply cover the area with
pads.  I started out with puppy pads, but realized that under pads (stuff
they put under bed bound people) work just as well and are cheaper.

Not using the box is usually one of two things, a medical issue, or a
behavior issue.  Cats prefer to go in a litter box.  If they are not, it
isn't to spite you (USUALLY) it is because something isn't right.  Figure
out what that is, and you'll fix the problem.

Please excuse my appearant top posting...
I am going to address a small thing I noticed below...

But first a short 'top post'
I didn't know the solution to your problem, but I took some of the advice
the others here as I was having the same problem with one of my two
sweethearts.

This is what caught my eye, my two cats are 'trained' to do a number of
things, including play fetch, shake hands, play dead, tell me when someone's
at the door, even hang my phone...

Cats aren't like dogs, note the quotation marks on 'trained' (above)...
while dogs learn from rewards and punishments... punishments defeat the
purpose, and often makes cats *worse*... They learn almost entirely by
rewards, you wait for things you like, Sammy, for example, just happened to
bring something to me, I made over him, petted and cooed over him... so he
started bringing more things to me... then one day I tossed it, and he
brought it back ! So I now have a cat 'trained' to fetch, after awhile, he
learned to fetch things I ask for !!!

Hint: reinforcement is absolute, you fail to do this, and the trick will
disappear after a while.

Just thought I would mention this.