I have assigned custom CSS class to let’s say Name textbox control in the ~\CMSModules\MessageBoards\Controls\Messages\MessageEdit.ascx file and it was rendered on the page without any problem:
<cms:CMSTextBox CssClass="xxx" ID="txtUserName" runat="server" EnableViewState="false" MaxLength="250" ProcessMacroSecurity="false" />
I do not see any reason why this would not work for you. Have you tried to restart the application? Could you please post your code changes?