1) it takes the better part of a day to update the server; took me 7 hours to update it to 1.2.5
2) all plugins we use have to be updated in order to update which is the reason why it's not updated yet
3) you should always keep a backup of your minecraft.jars. I have all the way back to 1.7.3
4) we have a vanilla 1.3.1 server up using a new map. Connect to: hawknetcomputing.co.uk:25566
----This map will not exist after the main server has been updated.