The fix is to make sure that when you have a counter rule in your css class, don't use spaces around commas, like so: counter(myCounter,upper-alpha);
as opposed to what I was doing: //breaks in IE counter(myCounter, upper-alpha);
When I apply the fix, IE9 seems more reliable viewing in IE9 standards mode. The jury is out if this is 100% reliable, but it's currently working. It's explained well here: http://jes.st/2013/ie7s-css-breaking-content-counter-bug/