Bud,

I have been mixing sound in churches for many years and we always turn off the gear at the end of the day. The brands I have used are Soundcraft, Yamaha and Mackie. Never any trouble of this kind with any of them.

Apart from some of the suggestions already raised, one problem that could occur in a church environment is if someone inadequately trained (or just not trained at all) switches on the equipment. With the general rule being that the power amps should be turned on last and turned off first, and that when turning on or off the volume of the amp should be set to minimum, an inexperienced operator could do some speaker damage turning equipment on or off in the wrong order. Of course, there are also plenty of other ways in which an inexperienced operator can blow the system, but that could be a reason behind the manufacturer's recommendation.

Hope this helps,
Mike