I just had an interesting experience with the standoffs on my Antec Sonata II case. Replaced stock CPU cooler with one that is held on with a screw-on bracket under the motherboard, and it was bowing my board. I went to computer store, manager said he never heard of such a problem.
I took the standoffs out and among other things measured them, and they don't meet the ATX specifications. ATX specification 2.1, in effect June 2002, years before my case was manufactured in 2006 according to QC date in the case, requires atleast 1/4 inch (or 6.5 mm) of clearance. My standoffs, not even close to 1/4 inch; I measured 5.5 mm. Went to Frys, got standard standoffs, they screw in just fine, they DO measure 6.5", and bowing problem solved.
Meanwhile I tried for almost a week to reach Antec's vaunted customer service. I called during their very limited phone customer service hours, and sat in Queue position 2 for 12 minutes. They don't even answer their phones. I submitted a ticket and it was ignored. I complained on Twitter and they said "phone us". I got an email that answered 1/3 of the questions I asked, told me to phone, and said they'd be glad to bill me for new standoff screws via paypal - but absolutely NO details on how to do that, and that was Friday.
One question he didn't ask is what are the specs on the motherboard screws, heh, heh, heh, wonder why he didn't answer that.
My guess is you also have a substandard case.
And I don't want to hear one word about Antec's vaunted whatever!