Just a little thought, do you have your Scratch disks set up correctly. You said that you changed the capture scratch to your internal drive, but do you have an insane number in the "Minimum Allowable Free Space on Scratch Disks"? It's also in the System Settings.
This could easily happen if you're following the good practice of not filling up your drives too much using this setting.
Hope that helps,
Ben
Curious Turtle Pro Video
Training | Editing | Support
Out Now - Film Wash Color Effects Vol. 3
& Mocha training for AE & FCP