Its because, up until recently, the national Authorities were supplied with question banks by the JAA. In the early days these were highly flawed and most of the larger Authorities kept their own local versions of the databases with edited questions and answers in them, plus their translated versions, plus extra questions in the case of some like the German LBA. When a new CQB was sent out they would import only the questions they wanted to use and run the exams from their local databases.
The Authorities (Greece, Malta etc.) without the resources do do this had no choice other than to import each new (and hopefully improved) version of the CQB in full and use the 'raw' questions. That's why you get LRJT flight planning questions in some states but not others.
As an interesting side point, I'm told that, now the JAA has gone, EASA have just discovered that they are neither funded nor authorised to hold a central question bank, so the whole thing is in limbo. My guess would be that the national Authorities will continue to hold their own local databases and we'll bumble on as normal.