I have a flash media player for my site and it came with .swf, .fla, and .as files.

The default skin is grey and dark grey, so I edited the .fla with Flash and changed the colors to blue and orange and exported it as .swf

Then, I uploaded it to my site, but the original colors(grey) show and not the edited version. I have uploaded it several times through Dreamweaver. When I open the file with Flash both locally and remotely the colors are blue and orange, but it is still displayed w/o color on the webpage.

I have refreshed the page many times and even deleted my cookies, but the new version doesn't show up.

I changed the name of the .swf this time, and it worked but I am not sure how that would change anything?

What do you have in your Publish settings in Flash ? Make sure you're not using Windowless Transparent.