I have the same thing. The doctor said I have IBS/spastic colon. I'm not sure if he's right or not. I also have the small pellet stools if I don't have the flat-sided and then rarely I am completely normal. I also feel I have colonic inertia. I ate a beet and it took 3 days to come out. I then gave up my coffee....ughhhh....to see if it was the caffeine causing my colon to spasm. It didn't help.
If I were you, I would get a colonoscopy to be sure.