I try to understand that you're using, preparative chromatography. If so, I think the problem is not your mobile phase, one posibility is that the amount of the substance of interest in the matriíz is very low .... however if the problem is that the analyte of interest is driven by the mobile phase, you diminish the percentage of water, however if the analyte staying in the stationary phase should increase the polarity of the mobile phase by increasing the percentage of water in the mobile phase.