If you don't set a buttonImg, and you specify a width/height, and make wmode transparent, uploadify loads fine, at the correct size, but the clickable area is the size of the canvas in the .fla file, so only a partial area of the button can be clicked.
This is easily fixed by modding the .fla to make the canvas, and the movie clip larger (I made mine about 200px by 200px, just to cover any size button I might like).
Also (more of a feature request), could you implement a parameter called methodOverride to set the header X_HTTP_METHOD_OVERRIDE, so that we can use this to edit datasets in a restful rails project? http://guides.rubyonrails.org/rails_on_rack.html – it's a nightmare without that feature, and I end up having to hack my rails code to work around it. Also the ability to specify cookies to add to the cookies header when posting would make uploadify the most awesome uploader to go with rails/restful auth. I know flash can't get browser cookies, but javascript can, and these could be grabbed in the jQ plugin. If you don't do this, then I'll write my own uploader that does!
This is not a bug, you need to set hideButton to true. No need to modify the .fla canvas
Unfortunately flash uploaders don't allow you to add headers. It's part of the flash security. If you wish to write you own uploader, then by all means go for it. It is not possible for us to write a plugin that everybody's needs, especially when there are one off requests. Please make sure if you use Uploadify as your basis you give recognition to Ronnie and myself for the countless hours we have already put in.