Something is a bit strange with the 2 different MASTER.csv files.
Lets take a shot at this. We use Hiraku Irabu from Japan as an example
In one you could easy see that he has a "starting" year of 1988, and the other is in 1997.
Then we look at batting.csv batting2.csv pitching.csv and pitching2.csv
He has "lines" in the real stat files from the year 1997 and in the neutralize stats files he has lines from 1988.
Then we asume we use neutralized stats for the dynasty of course.
We pick the year of 1990 as a start of our dynasty.
Now the problem starts....
Irabu will import in 1990 whatever master-file you use.

This will create big problem if you use the master-file there Irabu is starting in 1997 (the real year he came to US)
Since he has "lines" in the batting and pitching csv-files from the year 1988 he will ALWAYS import in 1988 whatever master-file you use.
THEN coming to the year of 1997 he will import AGAIN as a new player.
So summarixe will see Irabu in 1990 in both cases, but using the masterfile with 1997 as a start year we get Irabu numder TWO in 1997 in a Yankee uniform. Where the first Irabu plays we of course doesnīt know.
This was a fact I saw in old DB when the starting year in the masterfile isnīt the same as the first "line" in the batting.csv file. If you got different years you will get TWO players with the name Irabu.
This is a reflection of what I have experienced in many tries.
Of course the fact that I have done something wrong is almost close at hand, but I understood that it was just to pick one of the master-files depending on what you liked, have it named master.csv and then start.
I think the starting year in the master file MUST be the same as the "first" year line in the batting.csv and other csv-files or you will get doubles when doing import.