The above post doesn't add up to me...
The ACGME cites nearly every program for paperwork. If you don't file the forms exactly right, you'll get cited. Almost nobody goes through an ACGME review without something getting mentioned. Nobody gets put on probation for it.
There are some bad programs out there with glaring issues that still manage to get approved year after year. So there has to be a real reason behind the probation. Being critically low on certain disease site exposures makes sense. It would explain a lot of the other problems.
Residents not accurately logging cases sounds strange. The only thing I can figure is that they are critically low on certain disease site exposures, and are blaming the low number of cases on incomplete resident logging. Either way, that's something you can get cited for, but not something you're going to immediately get put on probation for unless it's true. I could miss logging cases here and there or I could mis-classify some cases (I'm pretty sure I have!), and nobody will ever know the difference. I always tell applicants that you don't want too much volume, but too little is bad also.
Not passing boards would be easily explained by not having enough exposure to disease sites. The in-service exams have everything to do with written boards, not oral boards which are more practical. Not taking the oral boards for multiple graduates makes no sense. Everyone wants to get board certified, when possible, as soon as possible. If multiple people are registering for the boards and not taking them, then they must be very scared of failing.
The majority of diseases are not treated with protons, or at least it would not be considered a standard treatment option to do so.