A bit more information... I decided to move from openELEC to Windows until the vdpau issues are sorted. I have openELEC ION RC1 installed on a USB stick and Windows 7 32bit Eden B3 on internal 2.5" HDD. PC is a Shuttle XS35GT. Booted into openELEC for the first time since I got flirc in the mail... Flirc 1.0 is waking my openELEC no problem, but not Windows 7.
When I get a bit more time, tomorrow I bet, I'll try flirc v5 to see if the random wake ups happen in openELEC.