WakeUp isn't waking machines

Help, my 1e version 5.5 Wakeup isn't waking up machines.  We have 1e with SCCM 2007 R2 and until April 17th was working great.  We initially found that the DB owner's password was correct and that's been resolved, but we have an Advertisement to Wake machines up starting at 5 am.  There are some machines that are waking up and I have 3 subnets that are giving me heartburn.  The ip subnets have been entered in the WakeUp Console, and they have a Primary and Alternate agents idenified.  The WakeUpAgt.log keeps alternating between Primary and Alternate agents.  I've reviewed the WakeUpSvr.log & the WakeUpAgt.log and nothing is standing out as a problem.  Is there documentation somewhere so that I can troubleshoot what's going on and get this fixed.  Thanks.
 
Joan

Generally speaking you should not enter subsets in the wakeup console.
Please let the server do that itself.
You are several versions behind which will make support a bit harder, any chance you can upgrade to the latest (6.0.500)?

Have you ever thought about using the Nightwatchman Console to do the daily wakeups and shutdowns??  That's what I do, I use the NWM console for the daily shutdowns/wakeups, then of course if I need SCCM advertisements to wake machines up then I set the Enable WOL in the SCCM advertisement.  It works very well.

Download WakeOnLanMonitor.exe & see if the WOL packaets are being sent out. have you tried using another tool to see if the machines wake? i.e WOL.exe.
  have you reinstalled the PC's? changed the NIC drivers?

To follow up more, see if the machines wakeup from sleep or from off. These are pretty different.
Waking from Sleep is usually controlled via OS/NIC settings while waking from Off is usually controlled in the Bios.