the vin wont shouldn't have anything to do with it not using the settings if there was a vin conflict it wouldn't start. lets start from the basics.
What year make model do you have? and osid of the bin or upload/link to the bin if possible.
What specific lines are you changing in the bin? screen shot or type word for word the table your changing.
I to have never had an issue where i successfully uploaded a bin and a setting not transfer. Are your fans set up correctly? IE are both fans connected in the stock configuration or has someone before you or yourself rewired them to operate at the same time? before i had a tuner i ran my 2nd fan off a relay connected to the first. but with the tuner i no longer needed to do this and set it all back to stock
