Can you pick one and wake it up and then post the agent log from the client and the EpoApSvr.log and server logs from epo for the time period when you do the wakeup.
Firstly, check the agent policy setting in the 'Logging' section: 'Enable remote access to log'
Has this option been ticked ?
Has the agent wake-up tcp/ip port changed ?
Has the same port been hijacked by another application ?
I'd take a look at the orion log at the same point in time as a failed wake-up call too.
There might be something worth seeing in that log too.