Thanks Benjamin for your input - it is part of the reason of the failure...
By default, AFT is configured to scan file size every 30 seconds, and to iterate 3 times over a file to consider it as static - very useful to make sure you will not transfer a file being currently produced and thus growing.
The point is that 3 * 30 seconds is 90 seconds, which is the minimum amount of time required to consider teh file as static.
If you need to catch them faster, and have no need to wait for a fixed size before processing a file with the same AFT CM, you can reconfigure it to say for example to scan every 10 seconds, and only twice, reducing the filewatch detection to 20 seconds.
Hope this will help other people facing the issue...