Make sure the last thing you do in the wizard (right before you save) is check the box. There is a current bug in the customization wizard that will uncheck that option if you do anything else afterwards. There is a note of the bug in the wizard documentation located here (see the note in section 6.2): http://www.adobe.com/devnet-docs/acrobatetk/tools/Wizard/installoptio ns.html#remove-installed-products
The note reads: "There is a current bug in which this checkbox becomes unchecked if any other feature is configured. Therefore, if you want to remove all versions of Reader, check this box as your last action before you save the modified package."