I heard that some of the issue with not being able to flash the tune through direct port was because the owner information was being entered into the computer wrong. Like if somebody had a full name of Johnathan Doe Smith entered when they started with APR, and the tuner enters John Smith, it was failing at the end during the final verification. I'm not sure how true it is, but I remember reading that somewhere. I think it was also because the car was initially tuned at shop A, car was sold and bought by new owner, was flashed again at shop B, and then for what ever reason the same second-owner didn't go to shop B again for v3, but went to a third shop(C), and the personal data, plus the shop code changing kept causing the system to double clutch and wiff.
And btw, mine flashed to v3 through the direct port the first time with no problems