No I think this is a SC code related thing. I remember Jsteed looked at the SC code and said it had quite a few memory leaks in it. So you ran a really intensive scenario with many missiles and many identical doctrines being loaded and reloaded into RAM for each missile - hence the slow down - then you start a new scenario but the game memory is shot to hell.
I suggest exit SC, let your PC settle down and then restart SC and try the defend the motherland scenario. I think you'll find all working.
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