Electrophoresis problem

[malurus]

Hi,
Some strange things are happening to my gels: there are differences in electrophoresis migration rate between individuals (of the same species) where there shouldn't be. The product involves an intron that should not differ between species, but can do among distantly related taxa.

It seems to be related to the amount of whole DNA in the sample, with samples that run faster having more total DNA residue in the wells (assuming that what is fluorescing is total DNA).

The PCR is a avian sexing protocol; the samples are extracted using an ammonium acetate protocol.

Anyway, I have attached a small JPEG showing the problem - has anyone seen or heard of anything like this before? Could it be contamination with salts, proteins etc??

Thanks in anticipation.

Steve