Thank you for this excellent tool. I've used it to develop MATLAB applications for a laser laboratory - interfacing and acquiring data from hardware, as well as data processing and visualization. Your toolkit has made things much more organized and has also influenced my decision to use MATLAB as a platform.
I have experienced the disappearing axes problem mentioned by Brett and M Koelemay. I have tested both their code snippets in R2011b and reproduced the behavior they report. I haven't investigated Brett's HBox position solution because my axes are buried several levels deep and don't know which Container to play with. M Koelemay's resizing suggestion works every time however.
Regarding performance, for complex applications the startup time is becoming a slight nuisance. This could be related to Holger's suggestion of removing obj.redraw statements. Perhaps a command which globally requests a deferral of redraws, until a partner command is called again? This could be placed in constructor/GUI initialization code.