Q: After adding fuel additive, SUV performed badly

After putting a complete fuel system cleaner additive into my gas tank, my SUV has been having bad performance. There is a rough idle, it hesitates when I accelerate, the muffler putters, and it has stiff brakes. I used the technique of running the gas tank until empty and then refilling it, but that did not solve the problem; it still exists. I am wondering if that means that it was not the additive I put in. Perhaps it is just coincidental that the problem started at the same time as adding the additive. Another thing that is happening since this started is that the check engine soon display on the dashboard is appearing. What is the cause of this problem and what can I do to fix it?