It looks like you are using Remote Power Control Utililty from here: http://communities.intel.com/docs/DOC-1767 ? If so, I have a have guess. This utility first tries to ping the system before it sends AMT commands. If the ping fails, the wake-up command is never sent. Something in your environment may be causing the ping to timeout or be blocked. What that could be, I don't know, but I'd guess it only happens when you try to wake all the systems at once. Exactly how to proceed depends somewhat on how everything works. If you can change the script that triggers the wake-up you could add some debugging like doing your own ping. You could also make a dummy script that just pings and see if you can prove my theory. Or, you could try replacing this utility with a sample utility from the AMT SDK (http://software.intel.com/en-us/articles/intel-active-management-technology-software-development-kit/). It's called remotecontrol.exe and it does basically the same thing that the above util does, except it forgoes the ping. Maybe it'll work better? One thing you also might try is to update the BIOS & firmware on one of the offending machines, just to see if it helps.
Hopefully that at least gives you a starting point. If you reply with more Qs, will you confirm that you are using the Remote Power Control Utility? If not, what are you using? Also, provide more info on how your AMTs are configured. IE - Small business mode? Using TLS and/or Kerberos? What provisioning server? Exact AMT firmware version?