Are you using one of the suggested protocols for CHO-K1? https://www.thermofisher.com/content/dam/LifeTech/migration/en/filelibrary/cell-culture/neon-protocols.par.56923.file.dat/cho-k1-ovary.pdf
We transfect pluripotent stem cells with the Neon. I have found that a plasmid concentration of 10 ug/ml works best. We had been using 50 ug/ml in our previous transfection system, but that was too much with the Neon. What concentration are you using for CHO-K1? Have you tried reducing it?
I am following the same protocol you mentioned here but my cell number was 2.4 * 10^6 in 100 mm dish. I have taken 0.5 ug/ml plasmid concentration. I cannot find out the problem yet.
I have changed the concentration of the plasmid to 1000 ng/ µl. When I was transfecting only one plasmid, the transfection efficiency was higher. But in case of double plasmid, transfection efficiency was very poor or negligible. What could be reason behind it?