I had the same issue with my JDM tune on my Saleen SC when I got it in 2009. JDM swore it wasnt the tune. I talked to them a few times with no luck. Got someone else to fix it.
Makes you really wonder how well these tuners really know what the hell they are really doing.
They don't. Just like jdm shutting off the knock sensors, citing they were too sensitive to the pd blower. The sensitivity of the ks can be adjusted down a bit, so it doesn't false trigger. Roush shut off the ks on the 4.6 engs in 2009 + 2010. There are tuners..and there are tuners.