Here are some things I did.  My cat hasn't had a problem like yours, but has
the occasional slip up.  She does now have an igloo type litter box with a
dome on it and she seems to like that one better than the other.  Once when
she had left a couple of little presents for me I noticed she had some still
stuck to her rear.  That never happened again, but perhaps she hadn't been
getting enough water or something and was having an issue of some sort with
that.  She has only gone outside her box to poo and only a few times.  But
most of them were when she was "mad" at me.  yesterday I came home and there
were three little gifts in the bedroom.  My apartment is undergoing some
renovation and I had to leave her in my bathroom for two days while they
came in to put new windows in my bedroom.  There's no way to block her just
out of the  bedroom and not have her in the way or trying to jump out the
windows.  She, likes to look out of them and when they are part way open she
sticks her head out as far as possible :)  Then I had to block her in the
back half of the apartment so she just had the bedroom, small hall way, and
bathroom for two days while they are doing the living room windows.  I don't
think she likes this :)  The other times, I had been gone for three weeks on
a trip to Italy and according to my friend who stayed with her while I was
gone, she was fine for a couple days (the longest I'd ever left her before),
mopey for another couple, then ok for the rest of the time I was gone.  Then
when I got home, for about three days she'd go in the box sometimes and not
in the box other times.  I think being distressed makes them do this too.
Just some suggestions as to what might be the cause.  If she doesn't do it
regularly, it's probably not a medical concern, but it wouldn't hurt to talk
to your vet just to make sure he/she agrees.

Beth