My son has been on probation in nj since Feb. 2012. He was just recently arrested for an incident that allegedly took place in Dec. 2011. I understand that even being arrested can be a probation violation, but does the fact that he wasn't "on probation" at the time of the alleged incident have any bearing on probation following through with a violation?

He should be OK as long has he called his PO the minute he got to a phone and explained it. Since one of the most serious non criminal violations is not reporting to the PO police contact.
So if he explains this he should be OK.