Keep in mind you had 14 psi in the stock tune and up to 22 psi in the Trifecta tune before you had issues. Now you say you have 8 with the stock and 17 with the Trifecta. Thus you've lost about 5-6psi in both tunes. Since the loss is about the same either way, then it is something else (most likely) that is causing the loss in pressure.
Larry, here is what I know about the LNF system. I don't have an LNF, I have a boosted LE5 and so I encourage anyone to correct any mistakes I have in my explanation that know the system better than I do.
The LNF's system uses a combination of Manifold Air Pressure (MAP) reading and manipulation of a Wastegate Control Actuator Solenoid to control boost output.
With a turbo setup like mine, you have the turbo's compressor housing (where boost is generated) connected to a wastegate actuator. Inside this actuator is a spring keeping the wastegate valve shut on the turbine side (exhaust) of the turbo. As boost builds, it starts to press against this spring. Once boost pressure is greater than the force of the spring holding the wastegate shut, the wastegate begins to open allowing excess boost to bleed out into the exhaust. This is what sets how much boost is produced by the turbo. The factory spring in the K04 turbo on your car is rated to about 6-7 psi on the LNF (about 4-5 psi on the larger 2.4 LE5). This is why when you go into limp mode, you only see about 6-7 psi of pressure.
As you have seen though, your car has been able to produce a LOT more than 7 psi of boost. This is where your ECM, MAP and Wastegate Actuator Control Solenoid come into play. The solenoid goes between the turbo's compressor and the wastegate actuator. It also has a reference line to the turbo intake as well that will always read a vacuum. See the attached diagram of this layout.
This solenoid can open and close to allow some or all the boost pressure from reaching the wastegate actuator. What happens here is your ECM is reading the boost level the MAP is sensing and comparing that to an entry in it's programming that basically says how much boost you want to run. When your MAP reports this boost level to the ECM, the ECM commands the solenoid to open and allow some boost pressure to go to the wastegate actuator and allow it to start opening in order to maintain the boost pressure the ECM is trying to maintain. If you have ever dealt with an electronic boost controller in another vehicle, that is what you are essentially dealing with here.
Now with the factory tune and it's "learn down" feature, the ECM is programmed to expect a certain torque output under varying conditions. When the calculated actual torque measurement for a particular condition exceeds the expected torque output stored in the computer, the computer will try to reduce power output so that actual calculated torque matches what is programmed into the ECM for expected torque output.
What this means is if, for whatever reason, the DDM intercooler allowed you to produce more power (due to better cooling of the air charge, better flow to allow more air to get sucked in to the engine with each stroke, magic pixie dust...whatever is allowing the car to make more power) the stock tune would reduce boost levels to bring calculated actual torque back where it thinks it should be.
On the other hand, the Trifecta tune is supposed to do away with the learn down feature and thus the ECM shouldn't be trying to reduce power output. Now I don't know if Trifecta kills the learn down feature in BOTH tunes...stock and their tune...or just in their tune but considering you're seeing the drop in both tunes I would suspect it is something else.
Hotter air temperatures can also cause lower boost readings. Hotter air = thinner air = less boost. 6 psi though would be a huge swing...like say going from 50 degrees to 110 degrees in temp. Better flow through the intercooler could also cause a reduction in boost. More restrictions mean higher boost levels and lower restrictions lower boost levels but since your MAPs are AFTER the intercooler, I'm not sure how this would affect readings. That is a question for someone who knows more than I. I'm still learning some of this turbo stuff too.
So when you're comparing boost readings, you have to compare them based off the same tune. If you try to compare base tune boost readings to Trifecta tune boost readings, you're always going to be off.