Strangely, my yeast colony PCR works only with Sapphire hot start master mix or Amplicon master mix but not by any other master mix, or if I individually add Taq polymerase with compatible buffers etc. Does anyone know how to fix this?
Check the composition of the two master mixes that work and see if you find something peculiar.
Also, common causes of PCR assays that result in no product are: missing reaction component; suboptimal reaction conditions (e.g., Mg concentration); presence of inhibitor in reaction; and contamination.
Colony PCR is definitely an issue with yeast as initial temperature induced cell lysis is very unefficient and aleatory due to cell wall resistance to the treatment. I always prefer preparing lyticase/zymolyase cell lysates (see the link below) prior using them as DNA templates for PCR.