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The one you buy from MyFico is EX FICO 08 Classic.
The one Logix pulled on you was probably EX FICO 04 Classic.
It seems to be that the smaller banks/lenders are still using the 04 models while bigger ones are using 08. I looked up the revenues of the banks that pulled 04 on me and compared them to the revenues of the 08 ones. Cap1, US Bank are the only ones that pulled 04 on me while Chase, Amex, Citi, B of A, Barclay's all pulled a variation of the 08 scoring model (Classic or bankcard enhanced). Out of those 6 banks, the two with the lowest revenue in 2012 happened to be the ones still using the 04 model. I don't know of anyone still using the 98 model which MyFico is selling here for 20 dollars..
Based on personal experience, 04 Classic and 08 Classic can have significant difference. On my most recent app spree, I had an 04 score of 666 and an 08 score of 762 on the same day. (96 point difference)
I don't know much about fraud alerts so can't help you there...