So I had this issue before updating to 10.10 and it persisted after the upgrade. I have a dual monitor setup. Each time I log in from a restart I have to tell it not be be a clone of the first and that it's to the left, as well as change it's resolution. Now with 10.10 and activities I have to switch that as well.
I have a dual boot of kubuntu and windows, so it's really annoying to have to set this up every time I come back. I've had a friend suggest there might be a config file somewhere that I could add a line to.