Joe, I only re-edited the 1st photo to brighten it up some. Everything else was accomplished by switching from Photobucket to Flickr. That did indeed solve the sharpness issues, and some brightness and contrast issues.
As for which programs I use to edit, I use Olympus Viewer 2, Nikon View NX2, and for HDR imaging Photomatix Essentials 3.1. I like to do my 1st rough editing in the Olympus program, then finish up with the Nikon program. Each has their strengths and weaknesses. I've been playing around with Photomatix with just one image, and under certain conditions does a super job.
The two Orange/Yellow Orchids are none like I've seen before, and actually have a deep color intensity.
As for your before and after pictures, I actually prefer the tonal qualities, as well as the overall image of the 1st one. On my computer screen (which I was able to see the full test patten I was sent the link to,) the untouched picture looks soft, has rich natural color, and was shot under diffused lighting conditions. the 2nd image looks as though it's slightly over exposed, and was shot in brighter and more contrasty light. The background in the 1st picture is much more pleasing and complimentary then in the 2nd photo. This is just my humble opinion, but you get a better idea of what I like in a floral.
Photography is more subjective then objective, as each viewer has their own sense of what they like and prefer, which doesn't necessarily coincide with others. Fine art is a perfect example of this.