[Bounty 200 RSC] Looking for Help With Low Transfection Efficiency in KO vs. WT Cells

Has anyone here dealt with lower transfection efficiencies in knockout cell lines than in the wild-type? 

I'm working with a U2OS  (human osteosarcoma) cell line which harbors a knockout for a protein I'm studying, knocked out using Cas9 RNP. I'm transfecting using Lipofectamine 3000 and an EGFP bearing plasmid (pcDNA3.1). I have performed an optimization screen of different concentrations and ratios of Lipofectamine 3000/DNA, and our knockout consistently has much lower transfection efficiency than the wild-type. It followed the same trend as the wild-type throughout the screen but just never generated as many transfected cells. 

I'm asking this because I want to transfect my cells with a FLAG tagged construct followed by co-immunoprecipitation, and transfecting the knockout cells to a higher degree is essential to that. I'm seeing ~5% transfection efficiency at max right now. Really hoping I won't have to resort to FACS to separate out transfectants. 

Looking For: Insight into what is going on, and how I can fix it. Protocols pertaining to this or papers which are informative about this issue would be excellent. 

Note: Multiple bounties are up for grabs if more than one response hits the mark.