What MSD are you using? I have the 6212 that i can control timing via a MAP sensor. I think its a 62112 that doesnt work to control timing in reference to boost.

The reason that the portfueler pisses me off sometimes is it is inconsistent. When tuning my car on the dyno, which took a total of about 20 hours and around 100 pulls, we would set the afr's and then without changing anything the afr's would change. However without changing anything we could do another pull and the afr's would be back on track. My best guess is that it is the stock computer doing its thing and the portfueler obviously doesnt compensate for any changes. Now granted the variations of the afr's from pull to pull were not that great; at most .3 or .4. But it is enough to get a little aggrevating sometimes when you are trying to dial something in perfectly.