I am having problems with...

      

SNP Not Amplifying

You cannot amplify a SNP.
 

Trailing Clusters

Not using ROX or not designating it as a passive reference dye may cause trailing clusters.
 

Diffuse Clusters

You have diffuse clustering in your SNP analysis.
 

No Autocalling

Failure of autocalling of SNP results is usually due to outlier wells or software problems.
 

Normal Allelic Discrimination Plot Example

Your cluster plot should look something like this.