Small batches generally end up being darker than expected, even programs like Promash aren't much help here. If you're using a program like that and homebrewing, I'd take whatever SRM they're saying you'll get and then add a few more points. If you're going for a lighter beer, aim lower.
If you're brewing commercially, I'd say use less specialty malts. Keep your long boil as the stability and quality of your product needs it, just remember that in most cases with brewing materials, less is usually more.