If you are using FSI brand socks, they contain "small traces of foreign chemical from the production process, this chemical is NOT harmful to the aquarium life". They suggest rinsing the sock well before using. This may be true for other brands as well.
I have been buying these bulk and did not rinse once. The result was similar to yours, skimmer went nuts and a lot of bubbles in the tank. This cleared pretty quickly and no livestock was harmed. I now make sure to rinse the new ones thoroughly.