Is your control transfecting with empty vector? If this is the case, did you prepare your miniprep for your control DNA with the same method as your experimental plasmids? I ask this because if you are using control vector from a company and then the others were prepared in-house there could be a difference if you did not use an endotoxin free plasmid prep kit.

I agree with Jared. Be sure that you prepared your plasmids in the same condition, and It should be better to prepare in a endotoxine free manner.

Can you confirm that you control condition is the empty plasmid (pcDNA alone)?

actually, we prepare all in house under the same conditions.