How are you checking the tube?

Pump the tube up to 2x or 3x its normal size. Then take a bucket of CLEAR water (or a sink full), and slowly rotate the whole tube below the bucket, one bit at a time looking for bubbles. There will be some bubbles from immersion, but make sure you also don't see slowly expanding bubbles on the tube. Also watch the valve.

It is quite possible you're not finding the holes.

Oh, also pay attention to the valve orientation with respect to the tire, so you can go back and find the cause of the flat in the tire. Little pieces of radial tire wire can be nearly invisible, or perhaps a piece of glass embedded in the tire.