You won't see your transaction show as confirmed until you catch up to the point in the chain where they were created.
No shit at that point in time the blockchain was at October 31 last year the addresses in that wallet having been in use since June 6 of last year according to the blockchain explorer which tells you when the address I checked first appeared on the network so there would have been a balance somewhere along the line there. It does now however show a balance so whatever funky foolishness this upgrade is pulling in the transaction database seems to be righting itself as it goes along.
Thanks gmaxwell, I know I should probably RTFM but would you happen to know a list of trusted peers to connect to? This is going to take another 2 days at this rate.
Try killing off then restarting the daemon to try and get some new peers, I've done that a couple of times so far and right now am at block ~179000 from starting with the upgrade a couple of hours before I first posted, another 1300 or so blocks and it will be done.