Hello Guillermo,
I haven't noticed such problem with web Designer you describe (no "y" position set). Have you tried the 'Validate' button and build the package in Guvnor? Do you have clear steps to reproduce the problem?
One tip - you can also try new BPMN2 Modeler for Eclipse: http://www.eclipse.org/bpmn2-modeler/
My 2 cents.