If the problem is persistent with different springs, then I doubt the spring is the problem.
Did you try adjusting the LPR? I've built a bunch of pneumags that can burst fire with RT on/offs, even with standard 850 psi output tanks. Even if you had it set up correctly before, it's possible the LPR crept out a little and hit some magical point where the piston pressure perfectly matches the RT strength.
https://youtu.be/wTrXxGP9T4s?t=2m28s
If that's the problem, turning the LPR up a tiny bit should fix it.