How big a size difference are you talking about? If you are talking about a few kb larger then I would not expect a lot of difference, but if say double or triple size then quite possible. Another thing to consider though is efficiency of plasmid isolation. As you get to larger plasmid sizes you may shear more of the plasmid or just not successfully isolate it during the purification process. Lastly it might have nothing to do with size but with the insert.