I was able to resolve this issue by editing your plugin. I know this is not the ideal way to do things. If you could add this small change to your plugin in some fashion in a future updates that would be great. Thank you for the great plugin!
I just changed the capability type drop-down to an input field.
Line 648
//From this:
<select name="cptm_capability_type" id="cptm_capability_type" tabindex="16">
<option value="post" <?php selected( $cptm_capability_type, 'post' ); ?>><?php _e( 'Post', 'cptm' ); ?> (<?php _e( 'default', 'cptm' ); ?>)</option>
<option value="page" <?php selected( $cptm_capability_type, 'page' ); ?>><?php _e( 'Page', 'cptm' ); ?></option>
</select>
//to this
<input type="text" name="cptm_capability_type" id="cptm_capability_type" class="widefat" tabindex="15" value="<?php echo $cptm_capability_type; ?>" />
yeah. Modifying the plugin code is not really an ideal way.
We are approaching a real stable v1.0 fast and I will try to get a working solution for your problem.
An input field is “insecure” because a typo here is making the cpt useless and we are aiming to make the workflow as “secure” as possible.
See https://github.com/jornbakhuys/custom-post-type-maker/issues/33 for the progress on this.