Do you have any other symptoms besides soft and frequent stools? Do you hurt any? What color are your stools? Do you have more gas or gas cramps? Do your stools smell worse than they ought to (if you can't stand the smell of your own poop, then it stinks worse than it should). Other side affects can all be indicators of what the source of your problem is.
I know after my gall bladder surgery that I could not digest red meat or pork. I eventually got to where I could, after I adjusted, but it left me with an appreciation that protein can be hard to digest. I don't know if protein shakes are as hard to digest as actual meat is, but it sounds like you're probably eating an increased amount of that too.
So, from what I know so far, here's a theory: you changed your diet too radically too quickly and you upset your digestive tract, made it work harder, made it produce more bile (which can cause loose, yellowish stools that burn the anus) to digest the extra protein. Bile can irritate the intestinal lining when there is too much of it. Once it gets irritated, it can take a while to straighten back out.
Calcium can not only help absorb excess bile and water in the intestines, it can also help soothe inflammation in the digestive tract. If there's not a problem with you taking it, try one or two calcium pills a day. The brand to use is Caltrate 600 w/ vitamin D because it has the right balance of magnesium and calcium (Inape has a whole long post on how it works and why) so that you get a little bit of a constipating effect. Since your stools aren't very loose, you may want to start with just one pill a day. If and when that starts making you constipated, cut it to 1/2, then stop taking it all together--the hope being that it will help your guts recover and you won't need to take it indefinitely.
Once you get straightened out, you might want to reevaluate your body building plan and decide if you want to risk the protein again. If you do decide to try it again, do it very gradually. I would suggest you up your intake of meat by an ounce or two not more than once a week and then when you are constuming the amount of calories that you want, then slowly add in the shakes--again, a small increase no more than once a week. If you start to notice problems, cut back and give yourself some time to adjust. If you don't adjust, cut back some more, and so on. If you adjust, try adding some back in again and see how you react. It may just be that your guts aren't able to handle what you're asking of them; not everyone's guts are of equal fortitude. Of course you could try and compensate and take calcium while taking a lot of protein to keep from having loose stools, but I personally wouldn't advise that. No need to make your guts work hard if they don't really have to. You don't want to mess them up and be like most of us here forever.