Maybe this is because of the September update? Personally I don't have admin rights to install the update so I cannot double check. However I can tell you the experience of my boss, who does have admin rights. He installed the update when the notification came up but then when he opened up the file with the filled map the colours were back to default. I told him I don't have the problem so he is back on the same software version as me.
I see this problem too in the Service (online environment) and posted about it here. Hopefully the developers notice this and will provide a fix for it.