Sorry, I don't have a solution, just a comment. A single VI of 1MB seems quite large and I wonder where all the bulk is coming from. It would be hard to believe it's all "code". Could it be that all your indicators (arrays, graphs, charts, etc.) contain huge arrays as default vaules? It might be worth clearing all, followed by "set current values to defaults" before saving the VI.
Go to "File..VI properties..memory usage". What are the numbers for objects, code and data?
