Intune 05 Dodge Magnum R/T issue

[mk_hemi]

I had just tuned my magnum for the first time after running the automatic updates on my mac (bootcamp) and once I tuned the car I had started up the car, and it ran extremely rough. I scanned the car on intune, would not show up any fault codes or even clear them. I had to plug in my scanner tool which came up with the p1411 and p1414. The scanner tool would not let me clear it either. I immediately flashed it back to the factory, started it up and still gave the codes. I ended up disconnecting the battery and resetting it. The car is running fine now, is there any particular reason why I ended up with the p1411 and p1414 right after flashing it and it completing.