Because you're working for the same company, in the Seattle office. Additionally, a lot of the difference is from income taxes that you no longer pay - something that companies take into account when making the initial offer, but not generally when doing transfers.
If you got a boost from transferring from San Fran to Seattle, overtime it would even out during merit pay-raises. Companies that are large enough to support development offices in both Seattle and Bay Area, are large enough to have a very formalized process for raises, which take into account your current pay vs the local market rate for that position.
From what I've heard from friends at big companies, the primary variable in the merit process is your current Salary - it does take the other things into account, but almost never enough to make as much of a difference as your current Salary. That's why people stress that it's so important to negotiate your starting salary higher, and not expect to get paid better once in the company.