I am not sure I can understand your question correctly. In an attempt to reply, I assume that your PCR products are less that 100bp and you have some difficulties to get reliable results, right? What kind of electrophoresis have you been working with, gel, capillary? If it is gel, you can increase the concentration of you agarose and/or use specific agarose to reveal small amplicons and increase the power of their separation. If it is capillary electrophoresis on an e.g. ABI, this should work from our experience.
first screen the few primers with different temperature (Higher then mentioned in primer sheet) and you can also try _Touchdown PCR_ to confirm the primers having complementary site or not.(specificity)
Because they may be primer dimer or any other contamination
and.....
it will be nice to other researchers in understanding if you upload the gel picture !!