I'm not a developer of MiKTeX nor TeXnicCenter but I'm a teacher how to use MikTeX (and TeXnicCenter). Some of my students have problems with their installation and asked me how to solve that. BTW are that usually students not following my installation hints ...
MiKTeX has a separate update system and a separate package system. To have a well working system you should syncronize your MiKTeX system as described in the documentation or on several answers here on the page.
MiKTeX had some problems with the two packages
mathtools. With a current version of MiKTeX theese problems are gone.
Conclusion from your remarks: You have a version problem.
Wild guess: two installed versions, portable and basic/complete?
The best way to get a running system with MiKTeX and TeXnicCenter is to install first the current MiKTeX (I prefere the complete version). After you have installed MiKTeX install TeXnicCenter. Now TeXnicCenter is able to recognize that MiKTeX is installed and is able to configurate itself.
Conclusion: If you installed a new MiKTeX for easy life install TeXnicCenter new. If not you have to check each entry in your TeXnicCenter for correct pathes to the new MiKTeX distribution!
That was the reason for my comment: "For me it sounds that you have a problem with different versions you are using. How did you install MiKTeX?"
Your last comment mentioned you had two versions of MiKTeX on your computer. That is not a good idea. MiKTeX is build to give you the possibility to update your system on the fly (if you want), but then you can only use one version on your computer. Or how could MiKTeX be able to syncronize the updating system and the package management system?
Best and securest way to use two different version of MiKTeX is to use two virtual maschines, one for each version.