Please explain your assay a little bit more in detail. GC-content of your primers, primer design, amplicon length, how have you chosen your gradient, MgCl2 concentration, DMSO concentration, SYBR Green or EvaGreen,...
I´m doing allele-specific PCR nearly every day. Maybe I can help you.
I am sure PCR is PCR. Maybe looking at a published work relating to allele -specific PCR could be of help, by looking at the optimization processes applied. Good luck.