I'm having stutter issues too in 5.3.1 within VE Pro. Majorly annoying. I've worked around this by using 5.3.0 for now, but the problem is that newer Kontakt libraries are requiring 5.3.1 and it's becoming frustrating.
Native Instruments is aware of the problem. See their email to me below:
Hello Sam,
This issue seems to be caused by a bug in the current version of the application.
Thanks for your report. We have referred this issue to our developers and will try
to fix it in a future version. As a workaround we’ve found that changing the
buffer setting may fix the problem. If not, the only fix is going back to 5.3.0
for the time being.
Nicholas
Native Instruments Support Team