Is it safe to assume you have tried putting the I/O shield on the mobo before putting it in the case to make sure that the shield does actually fit? If it doesn't then it is the fault of the manufacturer and I would recommend you contact them and let them know. Otherwise, must be the case/mobo combination.
This probably doesn't help at all but I've been running my current system for months without the I/O shield on and I don't have any issues with dust or poking things that weren't meant to be poked.. (dirty minds...). Probably helps that I have a massive heatsink below the ps2 ports though so I get better airflow without the I/O shield anyway.
Im not at all comfortable with the idea of no IO shield as there are in my motherboards case more then just a huge heat sink back there, some of the ports are only 1 port high as it were and around/behind them are SMD's and other components vulnerable to being poked.
Also IO Shield or not doesn't get away from the fact that the PCB of the motherboard itself gets distorted on fitting in the case with the IO shield and that distortion is what is causing the misalignment. And bottom line IMHO there is no excuse for this at all.
I will phone the retailer i bought the case and motherboard(and pretty much everything else) from tomorrow and see what they say i guess.