Hi Michaelangelo,

If FITC was slowing down the PCR product the products would appear longer, not shorter.

Short PCR products usually mean that the primers are binding at a different site than the one you are targeting. Or that the primers are unspecific, ie. that they target more than that one (or 3) regions. Thta is often acompanied by other bands in the gel too. Unspecific binding can sometimes be fixed by increasing the annealing temperature during your PCR - if the primers are more specific to your target than the other amplification, that is.

Did you design the primers? What is their melting temperature and what is your annealing temperature? Have you gotten the primers to amplify your target before?

These questions may help with solving your problem.

FITC as suggested above would have to speed up the mobility of DNA to appear smaller. FITC does not change the mobility of proteins  in PAGE gels so i think there may be another answer. If you are happy with your size standard then maybe there is a different salt concentration in size standard compared with pcr samples which might make a difference in the mobility in an agarose gel...are you using large amounts of betaine  ( Q solution) or other salt in your PCR?. Can we see a gel picture please? If it were just the larger band being the wrong size I might suspect regions of homology causing the dna to loop and have secondary structure problems which running in denaturing PAGE would eliminate