Did you enable the CIR header on the motherboards BIOS settings before installing the CIR drivers or after? The page on the suppliers site mentions after downloading the driver, you have to activate CIR in the BIOS. If it's anything like my iMON hardware which enables power-on from S5 state, a small amount of standby power must still be available after a successful shotdown so that the circuitry responsible for turning on the PC again will work. This means that the very first time it's all plugged in, you may not be able to turn the system on with the remote (or immediately after a power failure for example), it may need to be powered on first using the case button and powered down normally before full startup functionality is achieved. Just to check the remotes power button is working, will that initate a shutdown correctly?
Taking this into consideration, if you've followed these instructions, all is correctly enabled in the BIOS, remote initiated shutdown works and it's still not switching on from a fully powered off state, I think it's time to get in touch with your CIR hardware supplier.
The drivers for the CIR is included in the Linux system (OpenElec) but I guess they are not activated until the CIR is enabled in the BIOS.
The machine have been restarted and shut downing times after enabling CIR in BIOS and the shutdown from remote works perfectly.
From other fora it sound like there are more BIOS settings regarding the CIR on other/older Intel boards. Someone mentioned a setting for allowing the power on from CIR. In my BIOS there is only one CIR settings, which is enable/disable.
Maybe I should pull out the old trusty FlukeMeter and measure if there is power fed to the CIR header when the machine is powered off.
Anyone out there with a 4 or 5 series intel board who would like to check what BIOS settings you have regarding CIR?
The drivers for the CIR is included in the Linux system (OpenElec)
Not that I want to discriminate against a linux installation but have you tested this under Windows? I've not time to look at the moment but have you searched for Linux CIR drivers for your board on the Intel site (some hardware has Linux support and some drivers are avail - perhaps there's a newer Linux driver available which addresses this issue)? There may also be threads in forums dedicated to Linux which help.
I suspect the fact you are relying on native driver support, may be something to do with this as that's often a last resort if there are no newer drivers available (or in some cases if the newer manufacturer provided driver turns out to have a bug with advanced additional features not present on the basic native drivers).
If it's anything like the Soundgraph iMON hardware the drivers and software contain the code that the receiver should look out for and this is loaded into the receiver hardware memory when the PC is shutdown (standby power keeps the code in there while the rest of the machine is powered down). With iMON hardware if the power is completely removed from the motherboard at any stage, perhaps through a powercut, the remote won't work again until the OS and software is again loaded. I should emphasisie this may NOT be the way your hardware works so it'd be worth asking the supplier about their thoughts (and specifically if they can reccomend a Linux driver - maybe there's one on their website)?
Don't bother installing Windows if you want to keep the Linux install on at the same time. If you have a spare HDD, you could swap that in and put Windows on that just for testing purposes then swap back your Linux HDD. I think your best bet in the first instance though would be to ask the supplier about it. They're the experts with their hardware and if anyone knows all about compatibility between their hardware and Linux, they'd be right up there.