Simple Thread Inspection Tool : SITD

We produce about 10,000 M6x1 tapped parts every month. While delivering a 1,000 unit lot to our customer, they complained that the GO gauge: GP-6H found 12 pieces that were NG. We have not found any problems in our spot sampling when we check every 100 pcs. All the sample parts get a 100% inspection and are correct when using a thread gauge. We're not sure what else we can do unless we check every part which will add costs. Is there any other way to deal with this issue? I'm in big trouble.