My feeling is that there might be some subtle hardware differences between PCIII and PCV that mean the maps don't translate well. For example a value of 10 in the 15% column at 4,000rpm on a PCIII might result in a fuel mixture of 13.6, but maybe on a PCV the very same settings might result in a 14.8.
Basically the Power commander is a piggy back device. It tries to overlay an Alpha-N tune over a Speed-Density ECU (except at WOT, which is Alpha-N), which I believe means you're always effectively hacking it rather than really re-tuning it accurately. Add in some hardware changes between the PCIII and PCV (timing delays to injector pulses, or maybe less delays in injector pulses?), and the whole "map" goes to shit.
If I had the money, time, and inclination I would have built a custom ECU hardware solution for the 6th-gen using a Motec ECU. It's been done before (mainly for Honda outboard motors though). Then I would have sold it as a kit to VFR owners. Ah well, I bought a BMW instead.