In my experience, your powder problem would have to be very bad to cause a problem that significant, especially in a short period of time (less than a year). I have seen many different CTP/CTF systems run perfectly with very dirty spinner mirrors that haven't been cleaned in years. That being said, you should never put your system next to a press. It should be at least 10 feet away and in another room would be better.
In general, it is best not to over clean your optics. Once a year is usually adequate. The mirrors and lenses are delicate and easily damaged. Also manually turning the spinner can cause damage to it. There is no manual that can show you how. It is best that you be shown how to clean it by a trained tech.Have the tech show you next time he is in.
Also, the change in exposure you see may be based on the changes Mitsubishi has made to their materials over the last year or so. They also make the Mega materials that Presstek sells.