| | Re: PCR primer melting temperatures
WOW, I think I understand your problem. In the primer pair, they should be designed so that their melting temperature match, with a tolerance of 2-3C being OK, and 5C acceptable (these are just general rules of thumb). For the time being I suggest you test your primers with the commonly used melting temperature (95 degrees C) and whatever annealing temp that primer3 suggests, then optimize from there.
Primers are pretty robust, I remember doing diagnostic PCR assays using the wrong annealing temperature for about a year (and it worked fine), until I caught a typo in the literature and tracked it down (turns out the annealing temp was 4 degrees too high). By the way another rule of thumb is that the primer annealing temperature is usually 5-8 degrees lower than the predicted primer melting temp (not the 95C).