This isn't likely a driver issue since some machines work and some do not. Also, you are not likely to have a whole bunch of your network ports fail in the same way for a hardware problem. (Not impossible, but not likely.)
You have done quite a bit of troubleshooting, so I tried to think of something you might have missed that was not mentioned in your post.
The BIOS settings would not be part of the image you are using. Check for a wake on LAN setting in the BIOS. Make sure the BIOS in the failing systems is using the same settngs as the working systems. Are the ports enabled for remote management and is there a difference in the remote management configuration in the BIOS between the failing and working machines?
Check the MAC address on the failing systems and make sure that magic packets are being sent to those addresses.
I hope this helps.