Greg, I think your situation is probably a bit different. In my case, the issue really is VPMS. If I don't run VPMS, then the WoL works fine. For that reason, I have held back the deployment of VPMS. We did find that WoL is quite sensitive, but once we had experience with it, it worked OK.
The most obvious requirement is that the BIOS of the target machine must be set up to "suspend" in the right way,a dn to listen for the WoL frames. Are you sure your target machines support WoL?
The next obvious requirement is that the target machine must be in the same VLAN as the management machine generating the WoL frames. WoL won't work through a router! But you say you have a flat VLAN, so this cannot be the problem.
Thirdly, and this may seem an odd think to say, don't expect to wake up a machine unless is went to sleep connected to the LAN. If your ports are autonegotiating, then the autonegotiation needs to take place to set up the port. If you connect an already suspended machine to the LAN, then the port will not have been negotiated correctly, and you may not be able to wake it up. Same, or course, if you simply connect the PC and apply power without switching it on.
Check the port status on the switches shows "connected", I use CatOS, so the behahiour in my situation may be different from yours, which are all IOS, aren't they? Maybe that difference has some bearing on the problem.
That's is for the moment. Good luck, and post to let us know how you get on ... feedback, negative or positive, is always useful.
