Sounds like boost cut to me. If you datalog RPM, Boost, Boost Error, WGDC, it should be somewhat easy to see and relatively easy for your tuner to remedy.
The main culprit in my and others' experience, is usually over aggressive target boost below 3000-3200 RPM (in an attempt to maximize spool behavior) and/or overly aggressive WGDC Low and/or overly aggressive Turbodynamics, which tends to result in overboost in the more loaded taller gears. If your boost targets are realistic, much of the taller gear overboost issues can be made to go away, and if your WGDC Max are set up right, you'll still leave enough WGDC headroom to get good boost response in the lower gears.
I nearly had the same overboost issue w/ a protune I had from 2 yrs ago, running a VF52 and supporting mods similar to yours. I made small adjustments to WGDC Low but the main fix was specifying realistic boost targets.
My orig boost targets were like 12 psi @ 2000 rpm, 15.5 psi @ 2400 rpm, 19.1 psi @ 2800 rpm. My VF52 could never come close to the target boost at 2000-2400 rpm, so my Turbodynamics Integral would wind up immediately, then once I hit target boost around 2900-3000 rpm, the already wound-up TD Integral wouldn't decay fast enough to drop WGDC and I'd overboost to >22.5 psi, where the peak target was 19.1 psi. The boost limiter was set to just over 23 psi, so even though I wasn't hitting boost cut and tripping the P0244, I was seeing overboost-induced knock right after 3200 rpm, esp in cooler temps.
My main fix: based on numerous datalogs starting at 2000 rpm mainly in 3rd and 4th gears, boost targets ~2 psi @ 2000 rpm, ~7.2 psi @ 2400 rpm, ~11.7 psi @ 2600 rpm, ~17.8 psi @ 2800 rpm, and peak target 19.7 psi @ 3000 rpm. Now, I never overboost by more than ~0.75 psi in 4th, 5th or 6th (I have a Spec B trans/etc swap on my car), even when it's pretty cold out, and I consistently hit target boost by/before 3200 rpm in all temps I've tested in.
Last edited by serx7; 08-24-2015 at 11:11 AM..