I isolated mtDNA with DNeasy Blood & Tissue Kit (250) from buccal swabs and I got good results for a month. But after two months of DNA storage at -20 °C, pcr loaded on 2% Agarose gel shows primer dimers and some of the pcr samples don't work.
Did you try performing another extraction with the kit? If the template was not stored correctly, it may have degraded, although I have used this exact kit and my extractions, which are around three years old, are still working as they should. Have you made new working primer stocks in the case that it may be the primers which are no longer working or have become contaminated?
I guess it is not because of extraction kit. Overall stability of the DNA from buccal swabs is much lower than that from tissues. The reason might be the initial high amount of dead cells and as a consequence a high rate of free nucleases. Test the DNA from swabs for integrity on 0,7% agarose gel right after extraction and later on, and compare obtained profile with that from the DNA from other tissues.