A. SCCM 2007 offers two WOL configurations, which are configured on a per SCCM site basis—unicast and subnet-directed broadcast.
With unicast, a magic packet (a special-format packet that has a sequence of bytes—the client's MAC address—repeated 16 times, like someone waking you up by saying your name repeatedly) is sent directly to the IP address of the client. This would seem to be foolproof, but remember that when IP packets are delivered, the Address Resolution Protocol maps the IP address to the MAC of the client and switches maintain this ARP cache of mappings to know targets that it can deliver to. The target here is a machine that's turned off (we want to wake it up) and many switches clear out entries from their ARP cache after a period of inactivity, commonly four hours. So if a machine has been turned off for more than four hours, the switch no longer has a mapping of IP to MAC for the machine and can't communicate with it. This means the magic packet can't be delivered. If you're using unicast mode, check your switch configurations for ARP cache entry removal, because it could be causing you problems. Especially if it seems to work for some machines and then stop working if the machine has been off longer.
Subnet-directed broadcasts work by sending the magic packet to an entire subnet instead of a specific machine (such as <subnet>.255). All machines get the packet, but the repeated MAC address would only match one of the recipients and wake it up. This resolves possible ARP problems, but most switches and routers block broadcasts like this for security reasons, so the packets would be blocked at the routers or switches and never reach the destinations. To resolve this, you need to enable all routers and switches to forward subnet-directed broadcasts, which many network administrators won't do.
I've seen problems with both types of configuration for different reasons. You should explore your network configuration, specifically your network switches, to resolve or at least understand the problem, so you can use another WOL configuration or technology (vPro, 1E, etc.). You also need to check that your machines have the right configuration on the network card and BIOS to allow WOL.