This has to be because in 1.9 files were relative to their courses and in 2.x all files are relative to the activity/resource/forum/etc. they are linked in.
So I guess that the backup-zip-convertors or even the built in upgrade from 1.9 to 2.x will treat those backup-files in a legacy way because it would be much more complicated to convert everything to activity/resource/forum/etc. way of referencing the files.
Just a wild guess, Rosario