I found the problem cause.
The QIF exported file contains the parameter !ACCOUNT that separates the accounts transactions section.
Note. My CSV2QIF
installation language is French.
2006 version is a French version and to fix the bug I have to manually change/replace that parameter(s) inside the exported file and put !Compte .
By doing that it is working fine.
I’m interested by your product but I should appreciate that you have a fix about that before to buy.