There could be a couple of reasons why your PCR fails for a few samples.
- SInce you are adding template DNA from various sources, their DNA concentration could be variable.
- If you are using lysis solutions for your extraction, salt remnants can also impact how well your PCR works out.
- Also, you said that you DO NOT mix your gDNA into your master mix. Well, I always mix it.
- How gDNA do you add? Porbably would be a good idea to get you pipette calibrated if you pipette volumes that are less than 2 ul
Hope this helps.