Loosing boost

[justlearning]

2008 F350 with 6.4 Complete stock exhaust and air box removed. Installed AFE airbox. Using H & S tuner set to delete and mild as my objective is better fuel mileage. In the past week, 4 times after travelling 60 and 100 miles respectively, engine was idled for minute or two to cool down. Vehicle was shut off for a half an hour to possibly a couple of hours each time. Upon restarting, I had no boost. Reset tuner to stock, then back to delete gave me my boost which is lower than when using the stock air filter. This also cleared "Check Engine" light as it normally should. While driving the boost works proper. I removed the Afe air box. The turbo spins free by hand with no scrapes, screechs etc. The turbo linkage moves freely. All sensor connections are on and the ones removed from the stock exhaust are plugged into the wiring harness and zip tied out of harms way. The vehicle had worked for a couple of weeks before this malfunction started. No other mods to this vehicle.
I re installed the factory air box and I have my boost back which is higher than what I had when using the AFE air box. One suggestion presented to me was with the AFE, my turbo is running lean and could result in engine damage. This is one reason I switched back to the stock air box and to see if I would still have the no boost problem.
Any ideas what I may not have set properly or is there a software update I may need? Thanks for any help.

[justlearning]

Loosing boost update: Returned to stock air box and two road trips with no boost problem. All hose clamps were rechecked upon installation as were all visible engine sensors. Today I re installed the AFE air box, checking turbo for free spin by hand as well as the linkage. Re checked all hose clamps and sensor connection. Everything appears normal. Taking the truck for a short five mile run, the boost is normal and increases when using passing gear as it should. I have a few trips planned, so will monitor the boost. The boost worked normal the first while with the AFE air box then it wasn't there upon start up.

[justlearning]

Update: I did a trip yesterday, approximately 100 miles, AFE air box on, my boost worked as it should.