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Never mind.

Turns out the problem was AIM causing Notation to Hang.

When the computer starts, it starts AIM in the background.

If AIM is "stuck" then when I go to open a .NOT or .MID file with Notation is just hangs. As soon as I kill AIM Notation gets unstuck. But if I left AIM stuck and killed Notation and tried again Notation would be fine.

Very strange.