Hello,
As far as we are aware there is not bug nor nerf of these natures with 6p Pain. It is more likely you are suffering from a combination of three things:
1) Bad rng resulting in lower than normal resets. A single run isn't really a good sample size to determine how likely something is to occur. We'd need to do a hundred or more runs to be certain about the proc chances, and with the time that ii takes, this isn't really feasible. You may have also gotten extremely lucky on your previous run, so now you're seeing the high end and low end of the spectrum, which creates a big difference.
2) Power gain isn't as much as you might think. ii stats are based on the stats of the strongest player in your server. This means that if the strongest player's rate of growth significantly outpaces your own, you can actually do worse in ii as time wears on.
3) Lag. The mystery issue you are describing definitely sounds like lag. This can be mitigated by playing the trials in x1 speed and by ensuring you avoid certain ninjas, as well as making certain you do not interfere with the miniclient's processes.

However, it is possible the ninja has become bugged. If you can record a video of your trial with these issues, we can take a look at it for you.