Did you reset the amp block? Meaning, did you open the preset, go to the amp block, select a different amp model, and then re-select your desired amp model? You have to do that to reset various advanced parameters in the amp block that need to be changed for the updated algorithms. I can't guarantee it will fix the spikes but it's a necessary step after a major firmware update.
It also just occurred to me that we should create a new thread to discuss this issue, as we've hijacked the the 6.02 update thread.