Are you running Vista? Do you have dual monitors? Last question: do you have them stacked vertically?
The startup monitor position in Vista looks like this:

After every startup I alter the monitor position as follows:

Why do I have to do this? Why is this personalization not persisted? I really don't know. I presumed the much-touted multi-monitor support included in Vista SP1 would provide a solution, but alas, no.
I am curious to know others' experience. Keep in mind that I logon using a Limited User Access (LUA) account - although the behavior does not change when I startup as a member of local Administrators group.