Synchronized Publishing

EW2 you could sync no matter what.  EW3 changed it to what Den said above.  The sync button is avail when you press the Publish Web Site button

There have been changes made in EW3 to publishing, if you are using EW3 ?

This is a simple run down of the features related to publishing:

1.  If something is selected in your file list, pressing the appropriate blue arrow will copy just that one file.

2.  If your View dropdown is set to Changed Files, then you will only see the changed files and pressing the blue arrow will copy only those files (that have the blue arrow or question mark).

3.  If your View dropdown is set to Folders or All Files, then pressing the blue arrow will copy all of the files.

Basically, this is 'What You See is What You Publish'  So when you pressed the blue arrow with nothing selected and with the view set to Folders, it assumed you want to publish everything you saw, so it published your entire site.  That has nothing to do with whether Expression Web 3 recognizes whether things have changed or not.
As to why the Synchronize arrow is disabled in your scenario, it always is when you have the All Files or Folders view selected.  Synchronize is only intended to work when you are displaying just the Changed Files or when you have selected a specific file or files.  If you had changed your View dropdown or you had selected that one changed file, the Synchronize arrows would have been enabled. 

That is the way I see it, let us know if that helps.

Den