I'm suffering from the same problem.
Could you teach me the way to solve the problem?
I'm not using DOJO container, so I think my situation is the same as your one.
Thanks in advance.
Besides setting the width and height of the map, the width and height of each parent element must be set, from the map div all the way up to HTML. Leaving any layer height out will cause the map height to reset to 400px. Same goes for width.