Well actually I have no idea what can cause this. Can you be more precise on what is different?
What I think is that both logout and reloadui save:
- your saved variables
- your macros, frame positions etc (the text non-lua files in WTF/<account>/<maybe even deeper>)
And both on login and on reloadui, the addons and their saved variables are loaded.
Someone with experience of "Load on demand" addons might tell you if reloadui keeps them loaded, which could be a difference.
There might also be events that are triggered on login and not on reloadui.
There might also be (but erhm, it's going a bit far) addonmessages received by other people's addons when they see you coming online... but well that's not what I would call a huge difference
