Does Lipofectamine cause gene knock down?

[Kamalian, Laleh]

Hi everyone
I have come across this problem.  I have stably transfected my cells using Lipofectamine 2000 as the transfection reagent.  So far, I have been using my parental cells as the calibrator during transient transfection.  Now for the stable transfection I have used scrambled si RNA oligonucleotide to transfect my cells and used a pool of these cells as my control.  Using quantitative PCR to measure the mRNA of the colony cells and the control cells,  my colony cells show about 70% gene knock down comparing to the scrambled si RNA control cells, which is good.  However comparing to the parental cells, the control shows about 90% less expression of the gene of interest.  Once before during my transient transfection I had the same problem when used "no DNA" as my negative control i.e. Lipofectamine without any DNA.  At that time I had used western blot to measure the protein instead of QPCR.  I had noticed that my negative control lysate had considerable decrease in protein expression.  My question now is can Lipofectamine or transfection condition cause the gene knock down?  It especially doesn't make sense now that my scrambled RNA control cells have been growing in the selective medial for at least 4 weeks now.  I am thinking that even if the transfection condition had affected the cells transiently, it can't effect the mRNA level after being eliminated from the growth media.  Am I right or am I missing something in here? 
Laleh.