I don't mean to trivialize the situation, but this sounds like something that can be easily cleared up. if your credit card statement shows the double-charge, then I think you'll have ABSOLUTELY NO PROBLEM getting your refund. If you paid for the tickets, how could they have just been on hold?
Since this happened on both segments, there was obviously something wrong with your ticket. Having never had a problem myself (with their ticketing), I don't really know what would be the cause, but I suspect it was not the fault of the ticket agents.
Send your credit card statement and boarding passes. If you still have a receipt of the online transaction, that might be good to include too. I would ask for some additional compensation for the inconvenience on your SEA-SJC segment. And, ask that the "problematic" be deleted from your account (if it was ever actually entered

).
Bottom line...be proactive. Chances are nothing will happen unless you ask.
[This message has been edited by West Coast Flier (edited 10-03-2000).]