It sounds like backup is (unfortunately for you) working as designed. When a backup runs, it consumes a good bit of system resources. This isn't likely to be a problem with a modern multi-core processor, but a single-core processor will show the symptoms you describe. And if a computer is booted during the backup window, a backup may run immediately. The best I can suggest is to change your backup window back to the default midnight to 6:00 AM period, and leave the laptops in standby occasionally overnight. This way it's very unlikely that you'll notice any performance impact.
And you should also submit a product suggestion on
Connect, if a search doesn't show anything similar.
I'm not on the WHS team, I just post a lot. :)