I found it a little hard to believe that the holes on a mobo, which is advertised to follow a common standard, to be incompatible with the chassis.
Sure it can be a little wider or slimmer than the standard dimensions but the holes made on the PCB during manufacturing are exactly where they should be(note center to center hole distances) and are under stringent measures otherwise all the case manufacturers and/or mobo makers would go out of business if everyone had to drill holes into a brand new chassis or even worse onto the PCB.
OP,
FYI, if the engineer assigned to design the layout of the mobo messed up the hole spacings, he'd be drinking off the gutter - irrespective of owning 2 Engineering Degrees unless the company paid off people within ISO.
Just for kicks you can read more on the ATX standard here;
http://en.wikipedia.org/wiki/ATX
Hope your build turns out great as I was personally biased towards that chassis and some really awesome builds came out of it back when it was introduced
Don't mind me though, this thread has been solved with a brilliant answer only pointing this out since first time builders tend to make a similar mistake - this should help you out when another mobo looks out of standard in a regular case