I think there is some confusion here.
When your car was tuned, they should have only tuned the Hi-Throttle map. Using a dyno to tune Lo-Throttle on the SAFC is worthless and a waste of time. It is something that can be done at idle in your driveway.
Most likely, they only tuned your car for a WOT run, which would be the Hi-Throttle map on the AFC. You can change the Lo-Throttle settings until you're blue in the face and you won't effect the dyno settings, provided that the dyno shop knew what they were doing and used the correct map on the AFC. They would have also needed to set the TPS triggers correctly.
Sounds like your AFC Lo-Throttle map is extremely lean and should be corrected immediately.
Post up your settings and Ne Points for both the Lo-Throttle and Hi-Throttle maps and I'll help you along.
EDIT>
After rereading your post, it seems as though my response might need a little background to be understood correctly.
The SAFC-II has 2 different, independant maps that are based on throttle position. One is called the lo-throttle map and the other the hi-throttle map. At a user defined point, the SAFC-II switches from the lo to hi map and vice versa. You need to define this point within the SAFC-II. Most people set the low throttle point at 30% and the hi throttle point at 80%.
This means that when you are cruising around (TPS <30%) you are on the SAFC-II's lo throttle map. This map is set to maximize fuel efficiency by keeping the AFR around 14.7:1.
When you go WOT (or anything at a TPS >80%) the SAFC-II switches to the hi-thorttle map. The hi-throttle map was the one that was altered on the dyno. This map is designed for maximum power at a much richer AFR.....in my case 11.3:1.
So the company you took your car to should have set the proper throttle triggers and then tuned the hi-throttle map. They may have tuned the lo-throttle map for you, but it looks as though they didn't know what they were doing.
Do this, take a look at your logger and let me know what your FT's are at idle. Also, post up your settings on the SAFC-II.