If the operations of the two sites are entirely separate, it does not appear that there is necessarily an impermissible conflict of interest, but I would certainly raise the issue with the Board to be sure that the Board is satisfied with the situation.  You could be gaining significant information about sales, promotions, suppliers, pricing or other competitive issues that would allow you to enhance your site at the expense of the nonprofit’s, which could create a real conflict.  If anyone is concerned with your dual roles, you may want to drop one of them, or drop the similar items from your own website.