I'm running 10.10 and noticed this the other day, so it just started.
If I shutdown or restart the computer my desktop icons and panel icons all show up as what I think is the default theme. (It's ugly.) If I logout then log back in my preferred icons reappear.
I've checked that the correct icons are selected in the appearances' preferences and they are. I can try to change the icons during "an ugly session" to another choice but they don't change. The only thing I've found so far to get things back to the way I like them is to logout and log back in.
Has anyone else had this experience? Does anyone know how I can find out what is going wrong during boot?