And in case of Ubuntu what happened with USB devices? Could you wake up from USB or it was disabled too?
I have similar system withe same problem - USB Flirc receiver can't wake system.From what I understand the problem lies in BIOS/EFI -it looks like the ACPI wakeup tables are wrong. At /proc/acpi/wakeup there is XHC1 enabled only for S4 wakeup and not S3.
There is no workaround I know of.