Need Some Bulking Help...

To whom can help…

I am 31, 6’3" and currently 238lbs with approx. 20% BF. I’m in a bulking up phase right now and have questions pertaining to my metabolism-dieting-overall health. I am taking in 2900 calories/day based on a diet program given to me at Max Muscle store. I was 225 when I started the diet program 3 weeks ago.
The diet has me eating 6 meals/day.
265 grams of Carbs
284 grams of proteins
79 grams of fat

I am taking in more calories than the diet says due to my protein shakes having more protein in each drink than the diet says to consume.

I went to the doctor a few months ago and I was told that my thyroid wasn’t functioning at 100%.

I have gained 13lbs in 3 weeks with this diet and most of it is muscle, but I have noticed my stomach is getting bigger also.
Will my thyroid not functioning at 100% cause me to hold on to body fat?