If Tobias getting upset over the prank was valid then it shouldn't be surprising that he argued  with Severus over a punishment. Before, when Severus punished Harry for the runaway panther incident, it was easy for Tobias to tell Severus, well, I'd have spanked him, but you punish him how you like, because he wasn't the focus of Harry's misbehavior.  But now the shoe is on the other foot, so to speak, and Tobias loses it, and Sev becomes defensive, thinking his father is criticizing him as a parent, which is not something Tobias really should be doing, considering how he messed up in the first place.  Keep in mind that the two have very different discipline methods--Toby's old fashioned, old school discipline, Severus is a bit more modern, uses alternative methods for the most part, and sometimes the two methods don't jive.

As for the flashbacks, that actually is a common reaction to have for a victim of an abusive childhood.  Severus tells Tobias he hasn't had one in a long time, but I've seen Vietnam vets go through the same thing, they don't get flashbacks for years and then suddenly something--a loud noise, thunder, whatever, will trigger one and it's like they were reliving it all over again, and all the progress they made is gone until it's over.  That's what happened to Severus here, even though he has come to terms with his father and his past, there still are buried in his subconscious, pockets of fear and resentment, and under stress they'll emerge.