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Why is my plasmid DNA yield less for the pLKO.1 empty vector than it is for my pLKO.1 shRNA constructs?

While we cannot explain why, we also get lower yields for the empty vector than for pLKO. 1 shRNA constructs. We have tried transforming the pLKO. 1 empty vector into a couple of different competent cell lines and have tried making changes to the growth media and protocols but with no success in obtaining higher yields of plasmid DNA. We have been able to obtain 29ug of DNA using a HiSpeed Midi prep kit.