Here is what I'm using, user agent can be successfully set, while download preferences cannot.
Windows 7, Chrome 26, Selenium-dotnet-2.31.2, chromedriver_win_26.0.1383.0
ChromeOptions chromeOptions = new ChromeOptions();
var prefs = new Dictionary<string, object> {
    { "download.default_directory", @"C:\code" },
    { "download.prompt_for_download", false }
};
chromeOptions.AddAdditionalCapability("chrome.prefs", prefs);
chromeOptions.AddArgument("--user-agent=" + "some safari agent");
var driver = new ChromeDriver(chromeOptions);
Taken from chromedriver.log:
[1.201][FINE]:      Initializing session with capabilities {
   "browserName": "chrome",
   "chrome.prefs": {
      "download.default_directory": "C:\\code",
      "download.prompt_for_download": false
   },
   "chrome.switches": [ "--user-agent=Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/534.57.2 (KHTML, like Gecko) Version..." ],
   "chromeOptions": {
      "args": [ "--user-agent=Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/534.57.2 (KHTML, like Gecko) Version..." ],
      "binary": "",
      "extensions": [  ]
   },
   "javascriptEnabled": true,
   "platform": "WINDOWS",
   "version": ""
}
Check the temp Preferences file at *temp\Google\Chrome\User Data\Default\Preferences, no "default_directory" and "prompt_for_download" are set.
   "download": {
      "directory_upgrade": true
   },