Bookmarks syncing between 2 machines in Google Chrome after Time Machine Migration
Then my only thought remaining is that by doing a direct transfer of all files that there is a special chrome ID/profile that gets created when the app opens the first time. If that file gets copied then both computer have the same profile. You might have to export the bookmarks in chrome on one computer an then delete the ~/Library/Application Support/Chrome folder and then ~/Library/Preferences/com.google.Chrome.plist file in Preferences. Relaunch Chrome and that should force an ID/profile creation and then you could sync again.