Yes there was a problem with the top-slot and video card clearance during the inital release of this case. After some builders brought it to the attention of Antec they did tests with the boards in question and made a mid-production change to the case which corrected this problem. That was about a year ago if I remember correctly. Currently there are no issues like you have read in the past Here is an review stating the exact problem:
Taken from this site: HardwareGeeks -- Articles and reviews -- Review: Antec Nine Hundred
A little note, the Antec Nine Hundred has been revised the reason for the revision is that some graphics cards did not have enough clearance when using the first expansion slot, Antec has corrected the issue and is replacing the case for anyone who has this problem. So if you have this problem contact Antec. This problem only affects some Video cards that have DVI ports (Ed: which is 99% of cards nowadays...) VGA and HDMI are not affected at all.
Taken from this site: HardwareGeeks -- Articles and reviews -- Review: Antec Nine Hundred