It looks like this issue is due to a bug in the new Google Sheets, but you can use this simple script as a workaround.

- In your sheet, go to Tools > Script Editor. Erase the existing code in Code.gs and add this instead:

<!--HTML comment to get Markdown recognize codeblock after list-->

    function setCellAlign(range, alignment) {
       var ss = SpreadsheetApp.getActiveSpreadsheet();
       var sheet = ss.getSheets()[0];
       var cell = sheet.getRange(range);
       cell.setHorizontalAlignment(alignment);
     }
    function onFormSubmit() {
       setCellAlign("A1:F500", "center");
    }

* In the second-to-last-line, change <code>F500</code> to the expected bottom-right cell of your sheet. For example, if your rightmost column is G and you want to hold 1000 responses in your sheet, change the value to G1000 so the second-to-last line is 
   <code>setCellAlign("A1:G1000", "center");</code>

- Save the script project as "AutoAlign"

- Within the Script Editor, go to Resources > Current project's triggers. Add a new trigger for onFormSubmit, From spreadsheet, On form submit, and press "Save."

Your responses should now align automatically to the center. For whatever reason this script fails to work 1% of the time, but if that happens the next form submission will fix the previous row.