I believe this may be part of a new pricing test they are running - here is an email I received on October 14th, emphasis added is mine.

Dear SFO 1K,

To help you getaway, our always low fares will be on the move. We’re dialing down the dollars and turning up the fun. Grab a seat on Virgin America. It’s different up here.

Lowest available fares will fluctuate throughout each day, and sale fares will only be available at various time intervals during each day, for a total of at least 48 hours during the sale

Looks to me like you got caught with the fare changing during your buying cycle. As to the first scenario - VX refunds the difference from the original fare to the new fare, less a change fee. So if you were promised a full refund of the difference, they went above and beyond for you.