I just noticed mine doing the same thing last night. In my case however, I cranked the amp for only a minute or so and then brought the mast back to about half way (50watt head). I just figured it was because I ran the amp hot for a minute and it never readjusted.
OK, it is normal that the speed of the fan vary with the temperature inside the box. And it takes time to cool down so don't be afraid, that is normal.