I'm one of the interns at Cornell and it was definitely NOT work hours that got into probation - the most I've worked in a week is 82 (and remember it's averaged out over the month) and it's never been a problem.
One of the major reasons that we are on probation is because some of our seniors (in years past but also some of this year's chiefs) did not log their operative cases into the ACGME site and some of us didn't know how to log them in correctly. I know, when I was on the interview trail last year and heard programs being on probation for logging cases sounded sketchy, but the website is kind of hard to use; you look for CPT codes for a specific thing and then add modifiers to it; so for example for a D&C hysteroscopy case with resection of intracavitary fibroid for fertility I'd have to look for the D&C (non-obstetrical) code, then find the hysteroscopy code (operative, with or without removal of leiomyomata, etc), then click the infertility modifier. It's annoying and bean counter-ish.
Another one of the things the RRC found was that we were placing "service over education". Sounds bad, right? Well, what happened was that in the past residents were in cases and c-sections instead of going to lectures. But ever since the time my class came, they moved the OR schedules around the lecture times so that attendings know not to schedule cases around our protected resident lecture, M&M etc times or to expect no residents during those times, and it's worked out - those times really are protected. Also, they hired 2 new PAs at the Cornell campus (there are many PAs at Queens campus) that have been a tremendous help and keep us from holding the pagers during lecture times.
The program, from Dr. Chervenak on down (who has been meeting with each class every month or so to get input from us about what's been good/bad/changing/not changing), has been very much focused on whatever it takes to get us off probation and the improvements they have been able to implement are so swiftly/responsively and thoroughly that I cannot have thought things were otherwise. If you have any particular questions go ahead and reply to this thread or shoot me a PM =)