Jimmy,

Do you have the GenModel's Code Formatting property set to true and the
Comment Formatting set to false? If Code Formatting is set to true,
JDT should do the formatting, if it's set false, it should use the
preference's setting:

String tabCharacter =
options.get(DefaultCodeFormatterConstants.FORMATTER_TAB_CHAR);
if (JavaCore.TAB.equals(tabCharacter))
{
jControlModel.setLeadingTabReplacement("\t");
}
else
{
String spaces = "";
for (int i = Integer.parseInt(tabSize); i > 0; --i)
{
spaces += " ";
}
jControlModel.setLeadingTabReplacement(spaces);
}

Note that once it's messed up in the workspace, regenerating might not
fix it until you discard the local changes.