It makes no physical sense to do this, nor is the force field parametrized to include neutral phosphate groups in the backbone of nucleic acids. The pKa is ~2 so under all relevant biological conditions, the phosphate groups carry a -1 charge.
The issue you’re probably facing is that the effective concentration of the ions is enormous for this kind of system. I’d wager that even neutralizing ions are in the high mM or near M concentration. You may want to increase the size of your box to dilute these ions to something a bit more reasonable (of course this is more expensive to simulate, but also probably more realistic).
Plain cutoffs are entirely inaccurate and should never be used for electrostatics. Whatever you observe with a plain cutoff is fictitious.