I am not sure why you were using gedcom transfer from one version of BK to another. I just usually use the upgrade program included. My wife and I have been using BK since it's early days and love it. We have had very few problems and notes to the programmer (owner) of the company have always been returned in a timely manner. I bought my wife a Vista laptop for Christmas and BK6 seems to run just fine. We have not tried to import many GEDCOM files, so I cannot tell you what we would lose. With BK6 you have the ability to select the data you want exported (and to what fields in the GEDCOM).
Any questions - write me @ firstname.lastname@example.org