On my 2 GTX 460 rig, running v7.1.52, the ETAs for the two different cards are consistently differing about similar projects.
One card reports what seems to be an accurate ETA of about 9 hours, while the second card reports an ETA of over two days.
I thought I had gotten a problematic WU on one of my cards and not the other. However, both WUs finish in an approximately equivalent time.
Seems as if the ETA reporting is slightly amiss.