Tried here on Windows: just imported a MLV, exported to ProRes4444. i7, 4 cores, 8 threads, 3.64GHz, full 100% CPU usage. No idea what your computer does...
Is your files lossless or uncompressed? Lossless decoding is also single-threaded. But this small part should not drop overall usage to 30%. To what codec and option do you export?
Edit: thanks for update. Set smooth aliasing to Off and try again.