I had a problem running at wastegate spring pressure after I swapped turbos (going from VF39 back to stock TD04). The newer turbo had the vacuum lines already on it, so I used those. Turns out, those lines were missing the restrictor pill. I fished the pill out of the old lines, inserted in the correct vacuum line, and voila, hitting correct boost again.
If you haven't already, make sure that you have the restrictor pill in there, and in the correct line. If it's not in there, you could easily have this exact problem.
If the 06 is the same as my 04 as far as restrictor pills goes, this might fix your problem. If I goofed that up, my apologies.
Use this diagram for reference (where the pill goes):