This is a sometimes exasperating thing for me, and here's how I happily solved it.
After I complete a diagram, I export it to png and do a bit of touch up in the GIMP. I can align my boxes more accurately and add a pixel or two to my arrow heads. I can also cut and paste text from a box that got shoved to a bit larger size.
But what I love about this is that it forces me to keep my text very terse. I use the same size boxes on all my flow charts, and after having made hundreds I've found I can always compress and tighten and simplify the text to fit. If additional explanation is required, I place it alongside the appropriate box.
I realize this is probably not the "preferred" solution, but this creates lovely diagrams.
Thanks-
Jim Clark