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I recently encountered the same problem using Dreamweaver MX 2004. It's possible that this is a server issue. I manage several websites using two different hosting companies. Synchronize never worked on one of the hosts while it (until recently) always did on the other.
I have the same problem as you for the third time. The first time, I reinstalled Dreamweaver 8 and updated it again. I removed some extensions I had bought (blaming them). The second time, I was putting the files as a workaround until I found time to re-install. Then the Put quit working too. Suddenly, though, both problems cleared up. Now suddenly and with no know changes to DW8, the synchronization has stopped working again. This wonderfully easy, convenient web system is quickly becoming a PITA. I've never had the problem before DW8. There are no extensions installed. There seems to be something wrong in DW8.
I think I've found the solution.
To restore functionality, delete your configuration files. They are usually found at C:\Documents and Settings\<username>\Application Data\Macromedia\Dreamweaver MX 2004. (<username> is your Windows username)
Then open Dreamweaver and your site. You'll have to wait for the cache to be rebuilt, but your synchronize and put commands should work again.
DW MX 2004 here. I've recreated my site caches/configuration directory more times than I care to remember, yet still have problems synchronizing some sites. (e.g. I'm told I need to upload files that have not been changed nearly every time I do a site sync.) Yet other sites never give me a problem.
My conclusion, which seems to jive with Bolin: it's all in the server configuration. My personal websites function fine, but the ones I maintain for corporate clients are a PitA.
I'd advise Adobe to experiment with this feature, because it makes DW really frustrating to use in a professional capacity. Maybe some kind of automated file-lock/unlock to prevent the server from messing with our files?