When did the issue start? Did it coincide with a different cap or vendor? Different person setting up the machine
What about your cap supplier---what is their acceptable failure rate.....is it possible that their process is failing at a repeated time frame (after running x # of caps) and showing up as duds in your process. What is their inspection process?
Is it the caps that have failed, or is it that they are not on correctly, those are 2 different issues. Is the amount of torque used consistent?
Do you have lags in the air pressure used on the machine (if any) etc etc etc
If you already had some well established six sigma folks, you could solve this is a week or two.........without it, throwing darts with a blindfold
Have you contacted the capper manufacturer to come on site?