Saveas vs. File-->Save As ... More of a gripe than a question

Why is it that the "saveas" command, which claims to be the GUI alternative of File-->Save As, doesn't do the same thing as File-->Save As?

When I save the file as a JPG using the figure GUI, I get a great looking crisp image that rings in at 88 kB. HOWEVER, when I save the file using the saveas command, I get a crappy looking JPG that comes in at 123 kB!

I'm reading up on other options that suggest using the "print" command, but what's getting lost in translation between saveas and File-->Save As?

[Stephen Garner]

I'm having the same problem with creating images or PDFs using the programmatic version of saveas and print! The resulting PDFs or PNGs never look the same as the figure or the manually generated "point & click" equivalent, i.e. fonts are different sizes, tick labels overlap etc etc. I would love to see solution to this problem.