We have set our motors up for our launcher and they are not running at the same speed they were when connected directly through the battery when running through the motor controller, even when we replaced the battery. Is a power drop common when running through a motor controller?

While they will never be perfect, they should be close, provided that the two motor controllers are of the same type, and (if controlled by PWM) calibrated. Don’t necessarily expect (for example) a Talon SRX and a Spark to have the same voltage drop. Calibration is pretty easy; the directions are different for each controller type, but they’re in all the user manuals.

Are you using a encoder or something to measure the rpm of the motors or shooter wheels?

Yes, there will be a small voltage drop across the motor controller. CTRE has posted test data on their website.