specific loci not present depending on DNA extraction method? - DNA extraction and succesful PCR (May/23/2006 )

Hi, I've been using the Wizard SV genomic extraction kit from Promega to extract DNA and use it for PCR with mitochondrial primers.
The problem I've been having is that using the same template on consecutive days one time it will work and other times it wont work. Sometimes even though the positive control primers (ribosomal) worked, I have to extract DNA again and then it would work with my mitochondrial primers. Like if it were by "chance" .
Has this happened to someone else too?? where the specific segment of DNA to amplify is not present in the extract or perhaps is broken or something... although there's enough DNA in the extract??
PLEASE HELP!!!!

It happened to me once when amplifying some big chunk of some porcine DNA. Every second PCR gave me PCR product. No one in lab could explain it.