This may or may not be relevant, but if you have a boost guage, you may find that if you shift with just the smallest amount of throttle still open (not so much that it revs madly but just keep the guage off the lowest limit that it would go to on full closure) then you will eliminate the jerkiness, while full throttle plate closure will cause it. This keeps the turbo spinning and eliminates any jerkiness that might be brought on by compressor stall.
What happens when you are accelerating but are suddenly balked in mid-run and have to lift off just a whisker to reduce power - do you get a jerk or "stumble", possibly with an accompanying flutter from the turbo as well as exhausted air from the BOV??. This will help me to narrow the problem down.
"A jerky shift is still better than a shifty jerk"
CP_e Standback & PNP; CP_e 3" SS Downpipe; Corksport FMIC with Top-mount K&N filter & OEM Ram CAI; Turbosmart BOV; Dashhawk; Prosport Boost Guage; JBR solid shift bushes; DBA 4000 Wiper-Slot front rotors; Hawk Ferro-Carbon HPS Street front brake pads (@ 69,000km); Sumitomo HTRZIII's in 225/45 x 18