Likely, the problem was not the stop in the first place. It could be coating defects. Are you using a prewet? That will usually help, but if it does not, you may want to look into coating problems.
Stop is very very seldom the cause of pinholes. I wish I could dispel this myth. If there is a problem with stop, it usually causes blisters during processing which then dry down to a fish scale type appearance in the final film or paper. And, if stop causes a problem, it is usually due to extremely soft film or paper (a coating defect IMHO) and a developer that contains carbonate.