I've seen this problem come up multiple times, and had to talk to my bank when I got hit by it myself, but I absolutely understand why it happens. In our case it was because we moved from taking registration fees to taking accommodation deposits as well, and suddenly a large amount of money appeared in our account, and it does look very odd.

What I'd be interested in seeing would be somebody like eventbrite handling accommodation deposits and so forth as well as registration, then I could funnel everything through that. It's important that any such service release the funds to the event early so they can actually be used for running the event.