No matter how good they've gotten, mag-feds are ALWAYS rougher on paint than other guns. It's a big part of the reason why I stuck with the Zeus after fighting with the Tiberius line and TPX several times (I've owned 6 Tibs and at least 4 TPX's). Part of your problem could be the balls sticking together in the stack if you're going for a relatively long time between when you load them and when you use them, especially if the humidity is really high. Also, absurdly small paint might be allowing the 2nd ball in the stack to get clipped by the bolt, the Tippmann tongue-detent does allow some amount of roll-forward to occur.
For more cheap/effective TPX mods, see the link in my sig. Ultimately though, if you want a pistol that's reliable across pretty much any field paint you can feed it- I have to say to look for a Zeus. I honestly cannot recall over the past 3 years having ever chopped a ball with mine.