Gold should not form oxides from sitting around or
heating. Gold is a noble metal because it doesn't form many harmful
compounds. One thing that can occur with gold is it has a strong affinity
for sulfur. If there is a source of sulfur, such as rubber, or even
polluted air, you can form compounds that will start the discoloration
process.
In some cases depending on the solder paste flux being used I
have seen where during the reflow process of SiP devices the flux outgassing
across a gold pad will show some discoloration (easily described as oxidation).
Even after successful flux removal the stain is still evident on the pad. We
were able to remedy this condition and "brighten" the gold pads again
with an appropriate aqueous wash solution.
Also J.T. in your case what you could be seeing is the copper
layer underneath the very thin layer of gold changing color. It may have
leached or bled through microscopic copper particles during the plating
process. Now only the copper is oxidized and when the visual light refracts
across the gold it will look oxidized.
If you contact me and start by sending me a photograph of the
boards in question it is highly possible we can find a remedy for this
situation and recover this inventory.