Empty folders on remote server after synchronization

I am trying to set up a working environment for a very large web site and to get to the point of my post...
Whenever I try and synchronize my FTP with my local copy, I am selecting "Delete remote files not on local drive."
While the files are deleted on the remote server as they should be, it leaves behind empty directories all over the place where these files used to be.
The site is large enough that it takes over an hour to ftp it up to my testing server and I am doing a large amount of cleanup and deleting un-necessary files / directories all over the site. If I am going to have to manually track down every empty directory and remove them one by one, it is going to be faster to completely delete my FTP space and re-upload the site every single time I make some revisions which is a bit ridiclulous.
Isn't deleting the remote directories if I have deleted them locally considered part of SYNCHRONIZATION?
The site is so large that I can go grab a coffee while the synchronization is taking place but it is not quite as bad as re-uploading the entire local copy of the site every time I make significant changes to the site structure.
I guess this is related to why Dreamweaver throws "_notes" folders all over my site CONSTANTLY even when I have design notes turned off for my sites?
I have so many complaints about Dreamweaver and the fact that it pretty much has not improved much at all since Adobe took it over from Macromedia I don't know where to begin. I guess this would be a good place to start LOL!

As much as I hate replying to myself...
I was reading through this thread
http://digg.com/apple/OSXLeopard_Another_Serious_BUG_Unable_to_Browse_SMB_WindowsShares
I tried many of the suggestions one at a time. Unfortunately, I tried way too many suggestions to know if/which any single one was the "fix". The last three configuration changes I made were to disable IPV6, enable SMB sharing, then disable AFP sharing. After each of these, I did "sudo killall Finder" from a terminal.
Now it works for me as desired.
I hope this helps someone else.

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    Bill in Georgia wrote:
    After I synchronize, the style works on my local site but it does not work on the remote site. The color below the first image remains black on my published page.
    Seems to be working OK here. I see blue text.
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