thanks for replying, i think i found a workaround but i want to clarify the problem:
1 - MySQL is not case sensitive as far as table and field names - but will never create a table in uppercase
2 - Data Modeler with older Mysql version and driver was turning everything into uppercase : this does not prevent the query from running, but prevents Data Modeler to be able to link queries in a master - detail relationship and makes it very difficult to control the columns properties in designer.
3 - Data Modeler with MySQL 5 and latest driver surrounds with quotes anything that contains a capital letter, and subsequently fails to run the query, but leaves lowercase table and fields names alone. Therefore the solution seems to be to make sure that all table and fields names are only in lowarcase.